The Hero, the Princess and the Bounty Hunter
by BlueCharlieDeltaEcho
Summary: Calamity Ganon has fallen, yet a new threat has risen. One that could spell the end of the world and many others after it. One young hero and his princess may hold the key to their worlds salvation, but not without the aid of a renowned bounty hunter from a distant world, who knows this danger all too well. Metroid Prime/Zelda (BotW) crossover.
1. Chapter 1 The Anomaly

**Chapter 1: The Anomaly**

"When you light a candle, you also cast a shadow." -Ursula K. Le Guin

 **In an unknown dark area, blue luminescent liquid and tendrils begin to glow in an unsettling way before blue particles float from them and form a blue armored figure, which sinisterly laughs.**

 **Meanwhile, Samus awakens from a brief hypersleep in her ship to remove some moderate fatigue. Her last mission to the planet Zebes to retrieve the last metroid having been a failure and the result being the complete destruction of the planet, which in her childhood she once called home. All of this came to be too much for her to bear. The lasting wounds would be her failure to save the hatchling metroid which had imprinted on her as its 'mother' and its sacrifice to save her from the Space Pirate leader, Mother Brain, continues to haunt her seven months later.**

"Good morning Samus". The ships onboard computer, Virginia, says.

"Good morning Virginia, any problems while I was asleep?" Samus asks.

"None at all. Everything was shown to be normal."

"Excellent. Shall we take off then?"

"Acknowledged. Activating engines." Virginia says as the ship hovers above the hanger inside the GFS Olympus (Galactic Federation Olympus-class battleship) as it flies out into space. Samus then receives a message from the Olympus which Samus responds.

"Admiral Dane, thank you for letting me dock at the ship."

"No thanks required Samus; we thank you for all of your efforts in keeping the galaxy safe." Admiral Dane says. "If there is anything you need from the Galactic Federation, you only need to contact us."

"I appreciate that, thank you Admiral."

"Godspeed Samus." Admiral Dane says as the message ends.

"What is our next destination Samus?" Virginia asks.

"Well, are there any open bounties?"

"Checking…No known bounties in the current sector have been found."

"I see, and in other sectors?"

"Checking-"

"What is it, Virginia?"

"Samus, I have detected an anomaly from a distant planet. The energy signature being similar to other planets you have previously visited."

"Which planets exactly?"

"Tallon IV, Aether, Norion, Bryyo, Elysia and even the Space Pirate Homeworld."

"Are you certain?" Samus asks with concern.

"74% certain, Samus."

"….Virginia, set a course for this planet immediately."

"Very well, setting course for the planet. Entering hyper speed."

 **Samus's ship enters hyperspace as she heads for this unknown planet.**

* * *

 **Meanwhile, Two months had passed since the defeat of Calamity Ganon. The Kingdom of Hyrule was a far cry from its former glory, but the first steps to its restoration had begun. About two thirds of the castle had been repaired, and people were slowly returning to the abandoned towns to rebuild their homes from the ground up. The path had been long and painful, and they had lost many friends along the way, but things were starting to look better. Their sacrifices had not been in vain, and now, they could look towards a better future. Or so they believed...**

"Ahh, I hope that stops soon. How am I going get any sleep with that?" Link says in a grumpy tone, the thunderstorm outside disturbing his sleep. He then looks at the Champions weapons he was given on his wall. "Funny that 100 years wasn't enough apparently…"

The door opens up and Princess Zelda walks in. "Link, are you awake?"

"I am now. How can I help you?"

"Impa is coming. She and several other Sheikah are bringing something big to the castle. Can you come downstairs?"

"I'll be down in bit, let me get ready."

"Good. I'll meet you downstairs." Zelda says as she closes the door and leaves.

Link puts on his blue champions tunic with a Hylian hood and equips the Master Sword, Hylian Shield and Ancient Bow, having resolved to be ready for anything. He then heads to the front entrance of the castle and meets up with Zelda.

"Is all of that gear really necessary?" Zelda questions.

"Heheh, you never really know." Link responds.

"I suppose that's true." Zelda says as she holds the Sheikah Slate with the camera functionality ready.

"Anyway, what is Impa bringing?"

"She didn't say, just that she wants us present when it arrives. I just hope it can be studied." Zelda says with a smile.

"It's good to see that you still want to know about every little detail about every little thing." Link says in a jovial tone.

"It's just a small habit of mine."

"Right, a _small_ habit." Link says in a hushed voice as he remembers the 50+ journals that Zelda had filled with various entries on many different subjects and the samples of different plants she had him go and retrieve from faraway areas for her research.

* * *

 **30 minutes later, Impa arrives with several Sheikah and a large cart pulled by 12 horses. Impa had been a close friend to the previous king of Hyrule,** **Rhoam Bosphoramus Hyrule. Ever since his demise and those of the four champions, Impa has done everything in her power to be one of the strongest pillars in Princess Zelda's life after the 100 years of solitude to keep Ganon from wreaking further havoc.**

"Impa, good to see you again." Zelda says as she kneels down to hug the small woman.

"It is good to see you as well, my dear." Impa responds and then turns to Link. "You seem to be doing well, Link."

"I'm happy to see you too Impa." Link says as he smiles at her.

"Oh yes, before we show you what we brought, Purah asked me to give you this." Impa hands Zelda a rune.

"What is this?"

"It's a rune that she developed recently for the Sheikah Slate. She wanted you to install it as soon as we got here."

"Oh, well I better do that then." Zelda takes the rune and installs it in the slate.

"One more thing, she said to put the slate close to your face as the rune integrates into it."

"Why?"

"She just said it was very important that you do that."

"Alright then…" Zelda says in a confused tone as she has the slate screen close to her face. The rune completes its integration.

"SNAPPITY SNAP!" Purah appears in the screen.

"WAAAHHH!" Zelda screams as she tries to catch the slate from falling to the ground. "What was that?!"

"Hahahah! I got you Zellie!" Purah says from the Shiekah Slate.

"Purah? Why are you in the slate?" Zelda asks.

"In the slate? I'm speaking to you from the lab!"

"Wait a minute, how is that possible?" Link asks.

"Oh hi Linky! You want to know? It's the new rune I developed, I'm calling it 'Sheikah Eye', or by its code name; 'Eye Scare Zellie'. Admit it Linky, you thought that was great. Heheh!"

"Purah, you nearly gave me a heart attack!" Zelda pouts. "Link could never find something like that funny! Right Link?"

"No, of course not!" Link says as Zelda nods and then turns to look at Purah, Link gives a thumbs up at Purah while trying not to laugh, which she giggles at.

"Purah, her name is _Princess Zelda_ or _Her Highness."_ Impa says in an exasperated tone.

"Oh come on _Imps,_ Zellie doesn't care about it." Purah says in a carefree tone. "Anyway, with this rune, I can talk to you AND see you from my lab via the Sheikah Slate."

"Impressive. I didn't think you would outdo yourself like that." Zelda says with astonishment.

"Heheh, I may be a child (kind of) but I've got the wisdom of a 200 year old! Now, let's get to the main event. Imps, if you would be so kind."

Very well, and it's ImpA." Impa gestures to the other Shiekah to remove the cloth covering the large cart in the courtyard, revealing a deactivated Guardian Stalker.

"WHOA!" Link shouts in alarm as he stands in front of Zelda and aims an ancient arrow at the Guardian. "Princess, stand back!"

"Linky no!" Purah shouts. "It's not active!"

"Purah, why is that thing here?!" Link says as he lowers his bow.

"I had it deactivated to get it back to its original guardian protocol. Wait a minute; you're not still sour about 'that event', right Linky?"

"Do you have to bring that up again?" Link says in a resentful tone.

* * *

 **1 month earlier, the Hateno Ancient Tech Lab.**

"Just gotta slip in this shaft here and that gear there….and done!" Purah says excitedly. "Symin, it's ready!"

"Purah, are you sure bringing a Guardian Turret to the village is a good idea." Symin says with concern.

"We need to make up for the lack of security and a Guardian Turret would be perfect to keep those pesky bokoblins out, among other things."

"Yes, but what about making sure it doesn't misfire?"

"Hah! Who do you think I am? I just put in the information of any monster and the turret fires at them only when they are in the village or dangerously close."

"What about the intensity of the blast? It could damage nearby houses or harm the villagers."

"No worries. I can just lower the intensity if need be. Just like this!" Purah excitedly aims at the ocean to demonstrate the power of the turret, which malfunctions and aims at the village instead. "Uh oh…."

"What's 'uh oh'?"

"Uh, it's aimed at the village now."

"PURAH!" Symin shouts in panic.

"Don't panic! I can fix this!" Purah says as she aims the charging turret at a different spot. "Here it comes!"

The turret fires a laser blast at an unknown location.

"Gracious! What did you hit?!" Symin says with worry.

"Let me check." Purah uses the telescope to see around the village. "I hope I didn't break anything." 4 minutes pass. "Nope! The village is fine." Purah says with glee.

"Honestly Purah, you never take the consequences your actions take into consideration."

"Oh come on, nobody got hurt."

The door to the lab opens up and Link walks in, covered in black soot.

"Link, what in the world happened to you?" Symin asks.

"A laser fired at my house, it's virtually gone." Link says with an angrily quiet tone.

"Oh, did I get you?" Purah asks.

"….NO YOU DIDN'T GET ME! THAT WAS A GUARDIAN TURRET; IF YOU GET ME, YOU KILL ME!" Link shouts.

"Calm down Link. At least you didn't get hurt." Symin says with his hands up.

"What about my house?!"

"Uh…. OH! Look on the bright side; you can just move back to the castle!" Purah says with enthusiasm.

"Are you kidding me?! That house cost me 4400 rupees!"

"Really? This house only cost 2000 rupees. I'd say you got scammed."

"Purah…" Symin says disapprovingly.

"What am I supposed to do now?!"

"Hmm, just sleep here tonight. You can go to the castle tomorrow."

"I honestly don't have the strength to keep yelling anymore, I have to sit down." Link sits down at the table with an exhausted expression.

"Heheh, everything will be ok Linky." Purah says as she gives Link a cuddle.

"The champion's weapons were in there…"

"A decent polish will do them some good." Purah says.

Link glares at Purah as Symin pats him on the back to relax him.

* * *

 **Back to the present**

"Can we change the subject please?" Link says with an annoyed expression.

"Sounds good! Now, what I want to do is start up the Guardian again and have it be your sentry again."

"Can you do that?" Zelda asks.

"Well, they were only attacking us because they were controlled by Calamity Ganon. With that gone, they don't pose immediate danger to us."

"Well, I think we should give it a try then."

"Princess, I have my doubts about this. I have been close to several of these to know how dangerous they can be." Link says with concern.

"Link, the greater risk would be to try nothing at all and be attacked by hordes of monsters or worse; the Yiga." Zelda reasons

"Hmm, just stick close to me. Ok?" Link asks.

"Alright." Zelda then turns to Purah. "Now, what should I do to start it up?"

"Just grab that device with the eye symbol on it and say 'activate'."

"Very well." Zelda picks up the device. "Alright, everyone get back please. Now then, activate."

The Guardian Stalker lights up and starts walking. It then stops and stares at Zelda.

"What is it doing?" Link says as he reaches for an ancient arrow.

"Relax." Purah says. "It's waiting for a command from Zellie. Go ahead, tell it something."

"Uh, raise up one leg." Zelda commands and the Guardian complies by raising a leg.

"Unbelievable. It's actually listening to her!" Impa says with awe.

"Heheh. Hahah! I don't believe it, we have control again!" Zelda says ecstatically.

"Come on, make it do something cool!" Purah says.

"I've got it. Guardian, destroy that boulder in the field."

The Guardian aims at the boulder that Zelda points to and fires its laser, destroying it.

"Perfect! Link, what do you think?" Zelda asks.

"Well, it is kind of good not to be aimed at for once." Link comments.

"Well, what do you think?" Purah asks.

"So far, I see no problems here. This gives us a chance against our enemies once again." Zelda says.

"Hah! I'd like to see the Yiga try anything funny now." Purah declares.

"Wait, what's it doing?" Link says as he points to the Guardian, which is sparking and moving its head bizarrely.

"Purah, what is this?" Zelda asks.

"Hmm, it must be more damaged than I thought. No worries, just say 'deactivate'."

"Ok. Deactivate."

The Guardian then powers down and the legs go slack.

"Ahh, I was getting worried for a moment." Link says with relief.

"It was getting interesting too." Zelda says with disappointment.

"It's fine, I'll come by in the morning to check it out and see what got zapped."

The Guardian suddenly gets up and looks at Link and Zelda as its markings glow blue.

"What's going on now?!" Link says as he draws the Master Sword.

"DEACTIVATE." Zelda sternly commands. "Guardian, I gave you an order!"

"What is happening? It should be obeying you!" Purah says with worry.

"Guardian, I command you to deactivate now!"

The Guardian takes aim at Zelda.

"EVERYBODY GET BACK!" Link shouts as he grabs Zelda and ducks behind the pillars as the Guardian fires a multi-hit laser. "Since when could it do that?!"

"Link, it's aiming at Impa!" Zelda points out.

The Guardian readies to fire at Impa, who couldn't get away in time. Link shoots a bomb arrow at the Guardians head, making it shoot out into the sky and while that's happening, Link runs to Impa and gets her to safety with Zelda.

"Both of you stay here! I'll handle the Guardian!" Link says as he runs toward the Guardian.

"Link, be careful!" Zelda shouts.

"My boy, that is no ordinary Guardian!" Impa says.

Link jumps up and tries to run the Master Sword through the Guardians head, only to have it swipe Link away with one of its legs.

"ARGH!" Link then lands in rubble.

"LINK!" Zelda screams in alarm.

"Just what is this thing?!" Link says as he gets up.

* * *

 **Meanwhile, Samus has arrived at the planet and enters low orbit, viewing many ruins across the land.**

"What happened here?" Samus asks as she views the ruins that litter the land, along with many unknown destroyed machines

"Origin of the ruins unknown. Carbon dating indicates that they have been here for many years." Virginia comments.

"Are there any lifeforms around here?"

"Apart from local flora and fauna, there is nothing else detected in the vicinity."

"What about other areas?"

"Scanning….Samus, human life signs have been detected 21 miles to the east. Along with a faint energy signature we have been following."

"Good. Let's go to that area now. Maybe we can get some answers."

Samus flies to the east and after 4 miles, the alarm goes off.

"Virginia, what is it?"

"Warning. An unknown burst of energy is rapidly approaching towards the ship."

Before Samus can dodge the shot, it hits her ship and she begins to lose control.

"We're hit! Virginia, start emergency landing while heading for the source!"

"Understood." The ship activates the thrusters. "Destination is 11 miles away. 10 miles…. 9 miles….

"Come on, you can make it…" Samus says with determination.

* * *

 **Back at the castle, Link has managed to cut off two of the Guardians legs and already begins to show signs of fatigue. This Guardian being unlike anything he had ever faced before. Its integrity much stronger than others and its firepower many times more lethal.**

"Goddess above. How much can this thing take?!" Link shouts.

Just then, Link notices the swords strewn about the courtyard catching the lightning bolts from the storm. An idea comes to Link.

"Alright, you overgrown trash can. I've got a big surprise for you." Link says as he runs from the shots fired by the Guardian and grabs a sword from the ground. He then fires a bomb arrow at the ground to cause an updraft to propel his paraglider above the Guardian. Link draws the sword he previously picked up and throws it at the top of the Guardians head. Seconds later, a lightning bolt hits the Guardian, damaging and stunning it.

"Very resourceful." Impa says.

"He's good at that." Zelda happily says.

"It's over!" Link fires an ancient arrow at the Guardians eye, pushing it towards the rubble in the courtyard. Link then safely lands on the ground.

"Link, excellent work!" Impa congratulates.

"What was that about though? Why did it go berserk?" Link says.

"We'll figure it out later. Come on, we need to get your wounds looked at." Zelda says.

A laser then hits one of the pillars causing Link to turn around to see the Guardian standing.

"Get back inside!" Link shouts as the Guardian pins him to the ground.

"Link! What the-". Zelda tries to run towards Link as a group of Shiekah grab her and Impa and take them into the castle. "Let me go! He needs my help!"

"I cannot, your Highness." The Sheikah says. "We need to keep you safe."

"I said let go!" Zelda manages to escape his grip and runs towards the entrance.

"GET BACK HERE!" Impa shouts to Zelda.

Link looks back and sees Zelda running towards him.

"Princess, get out of here!"

"I'm not leaving you here, Link!" Zelda declares as she tries to summon her power, while the Guardian aims at her.

"NO!" Link shouts as the power wells in the Guardians eye.

Just then, the Guardian powers down its laser and turns its head 90 degrees to the right, causing Link and Zelda to see what it's looking at; an orange meteor.

"Is that…a meteor?" Zelda asks.

"It's coming towards us! Princess, get your head down!" Link shouts.

"AHH!" Zelda ducks down as the meteor crashes into the Guardian, destroying it and continues towards the castle ballroom, where it stops at last.

"Destination reached…. Energy confirmed…. Source:….Pha…zon…." Virginia says to an unconscious Samus before deactivating.

Link gets up off the ground and runs towards Zelda.

"Princess! Are you alright?" Link kneels down and asks.

"Yes, I'm fine. What about you?"

"I'll live."

"What in the world was that? It crashed into the castle."

"I don't know. It looked like a meteor."

"Let's get Impa and the others and check it out."

"Alright, let's go."

* * *

 **Moments later, Link, Zelda, Impa and the group of Sheikah head to the ballroom. Their curiosity having turned into complete shock upon witnessing that the object that had crashed into the ballroom was never a meteor at all. But something else entirely.**

"Link, are you seeing this?" Zelda asks in disbelief.

"I see it, but I'm having a hard time believing it." Link responds.

"Everyone, this is no meteor; it's some form of…machine." Impa says.

The three look at the crashed ship in complete astonishment.

"What is this thing?" Link asks.

"I think the real question is; where did it come from?" Zelda asks.

* * *

 _To be continued_

 **Authors note: Well, I finally started my second story. I know it probably sounds odd to combine Metroid and Zelda, but honestly the idea came in a dream, probably after finishing Breath of the Wild and seeing the teaser for Metroid Prime 4 shortly after. Needless to say, I was very excited by the news and couldn't stop thinking about it, Hahah. Anyway, I'd like to thank Fox McCloude for the pointers on "low orbit scanning" to make it more realistic, thanks buddy. ^_^ Once again, rate and review please!**


	2. Chapter 2 The Visitor

**Chapter 2: The Visitor**

"In the darkness is the light" -Mackenzie Phillips

 **In the (once again) ruined castle ballroom, after a few minutes of apprehension, Link decides to investigate the ship that had crashed into the castle.**

"Alright everyone, I'll check it out. Stay here; just be ready to jump in if I call." Link instructs the others waiting in the entrance to ballroom as he cautiously walks towards the ship.

"What is this thing, lady Impa?" One of the Sheikah asks.

"I don't know…" Impa answers as Zelda walks towards the ship, ignoring Link's warning altogether. "Princess! Get back here! We don't know what that is!"

"I know. That's why I'm going to find out." Zelda answers while readying the Sheikah Slate.

"Why does that girl never listen…?"

"Hmm, it's made of glass. Maybe I can break it." Link has approached the cockpit and draws the Master Sword to break the damaged glass. "Here goes- *shutter click* what the?!" Link turns around to see Zelda taking pictures with the slate. "Princess? What are you doing here? I said to hang back."

"I wanted to see what this machine is. The curiosity got the better of me. Now let's take a look, ok?" Zelda says while smiling.

"Ugh….Just stay alert." Link readies the sword. "Stand back please."

Link hits the cockpit several times before finally breaking the glass, revealing even more complex machinery within, along with the unconscious pilot.

"What is all this? What do these markings mean?" Zelda says with intrigue and she takes more pictures of the ship interior.

"Wait a minute Princess, there is something else in here." Link says while reaching out to the pilot. "Give me a minute."

"Well, what is it?"

"You're not going to believe this. But it's a metal human." Link says with amazement while pulling out the still unconscious Samus from the ship.

"What in the name of Hylia?" Zelda asks in complete astonishment. "Impa! Everyone, come here, you have to see this!"

Impa runs over with the Sheikah to the ship. "What is the matter Princess- what is that?!"

"It's some sort of humanoid machine. Is it some unknown type of Guardian?" Zelda asks.

"I've never seen anything like this before. If there is anyone who might know anything, it would be Purah. She's been studying our ancestors longer than anyone else." Impa comments.

"Purah? Oh my gosh, PURAH!" Zelda realizes that her communication with Purah was interrupted following the trouble with the Guardian. She hastily pulls out the slate to call Purah.

"ZELLIE! What happened?! Where is Linky and Imps?!" Purah asks with panic and fear.

"I'm so sorry Purah, I meant to contact you. Don't worry, they're both fine. Link, Impa come here." Zelda calls out to the two so that they are in Purah's view.

"I'm right here Purah." Link says

"Sister, I am well." Impa reassures.

"Whew, talk about giving a little kid a near heart attack. Anyway, where's the Guardian?"

"It's destroyed, thankfully." Link responds.

"Linky, you look terrible." Purah says, earning a small disapproving glare from him. "Did you destroy it?"

"Kind of…" Link says hesitatingly.

"What do you mean, 'kind of'?"

Link takes the slate. "Uh, _this_ finished it off." He points the screen at the crashed ship, which Purah looks at in shock.

"WHAT. THE. HECK IS THAT?!" Purah exclaims.

"We were hoping you could tell us, dear." Impa cuts in.

"How should I know what it is?! I've never seen that before! Where did it come from anyway?"

"I don't know exactly, the only thing I can say is that it came from the sky." Zelda says

"The sky?"

"Yes, it came down and obliterated the Guardian. Then it crashed into the ballroom."

"Wow, that's one heck of a story…"

"Actually, that's not the only thing. This was inside of it." Link lowers the screen down and Purah sees Samus on the ground.

"A machine human, or something?" Purah asks with intrigue.

"I guess it is. Its face is just a green T-shaped light with a red head; it has orange-yellow armor and some sort of cannon on what should be its right hand." Link says.

"Hmm, I see. What are you going to do with it?"

"We haven't decided yet. Why?"

"Can you put it someplace where I can check it out in the morning?"

"Wait, you want us to keep it in the castle?"

"Just until the morning, after I take samples of its metal in the morning we can take it apart and then dispose of it."

"I don't know if the Princess would want that-"

"We can have it placed in the library." Zelda interrupts.

"Of course she would…" Link says dejectedly.

"Oh come on Link, aren't you curious as to what this is or where it came from?"

"In a sense I am, but what about the security of the castle? What if it activates while we're sleeping?"

"We'll have sentries posted outside the door to the library just in case something happens. Would that calm you down?"

"Hrmm…..Alright, but just one problem from it and I will destroy it. Are we clear?"

"Very well. Purah, we're going to put it in the library. Will you be here in the morning to check on it?"  
"That's right. I'll be there first thing in the morning to see it and the machine it came in."

"Good. We'll have it moved now. We'll talk in the morning Purah. Good night."

"Be careful you don't throw out your backs carrying it!" Purah jokingly says before ending the communication.

 **The group exits the castle, two of the Sheikah carrying Samus out towards the library, with great difficulty as her suit is surprisingly heavy (Purah had a point). On a side note, both Link and Impa had to escort Zelda out of the ballroom, mostly because she wouldn't stop taking pictures of the ship or trying to get inside of it to see its mechanisms, much to Zelda's disappointment.**

* * *

 **Back in the Princess's room, which was once the king's room but is now occupied by both Zelda and Link, with a large curtain dividing the room so that they can have their own privacy in it. Zelda's side of the room contains a bed, bedside drawer, a large closet with many different outfits (Which Zelda kindly allowed Link to store his armors as well, that he acquired throughout his quest to stop Calamity Ganon) and shelves containing many, many journals which Zelda had written on many subjects and several plants which Link had collected for her. On the other side, Link has a bed, a desk, a small rug, four mounts containing the weapons of the champions that were gifted to him by their respective village leaders (which Link had thankfully managed to retrieve from his destroyed house), which he treasures as they are all he has left of them and finally a shelf containing the paraglider (as a memento from the king), Hestu's gift (which he mostly regrets in hindsight), a pet hot-footed frog (which he had comically put a sign over its cage reading 'Princess, this is not for tasting') and finally the bow of light that allowed him to defeat Calamity Ganon (which, of course, Zelda bestowed to him).**

"Ahh, darn." Link winces in pain as he dresses his wounds from his earlier fight. Not having attended to them due to the appearance of the ship.

"Link, do you need any help?" Zelda says from the other side of the divider.

"No thank you, I'm almost done." After finishing, he puts on a white tunic for sleep. "Hey, what did you think about tonight?"

"You mean with the Guardian and the machine?"

"Yeah."

"Well, I don't really know what to think. That Guardian, for one, fired its laser in a rapid fashion; I thought that they couldn't do that. Also, its markings glowed blue, what was that about?"

"You have a point, that was very out of the ordinary. It had more capabilities."

Now, that machine crashing into the castle. What is that?"

"Well, hopefully Purah can give us some answers about it tomorrow." Lightning strikes outside again. "Argh, what is it with this lightning?"

"You still don't like the rain, do you?" Zelda says in a sympathetic tone.

"It just reminds me of…past failures."

 **Link remembers the aftermath of Ganon's attack in which the king tragically lost his life, along with the four champions and an unspeakable number of soldiers and civilians, resulting in him and Zelda running for their lives in the pouring rain. Seeing Zelda in pure agony over failing everyone who counted on her was carved into his subconscious. Moreover, before losing consciousness after Zelda had awakened her power to save themselves from the attacking Guardians, the last thing he saw was her distraught face, pleading for him not to leave her. She only heard one sentence from him:**

" **I'm not going anywhere…"**

 **The next thing he knew, after recovering his memories, 100 years had passed.**

"Hah…." Link lets out a heavy sigh.

Zelda walks over to the divider and moves it aside so that she can speak to Link directly, who is sitting on his bed.

"Link...apart from my father and the champions, do you...remember anyone else that was lost in the calamity?" Zelda quietly asks.

Link looks down for about 5 seconds before finally facing Zelda. "I remember all of them." He quietly says with melancholy.

Those words hit Zelda like daggers on her heart. She now sees that she isn't the only one with haunting memories of the past, that no matter how hard they try, do not want to go away. Zelda looks at Link with sadness in her eyes.

"If it's all the same to you, Princess, I think we should get some sleep now. It has been hectic evening after all."

"Yes, you're right…." Zelda walks up and places a hand on Link's shoulder, causing him to look up in surprise. "I will see you in the morning. Good night Link." Zelda smiles slightly.

"Yes, good night. Princess." Link responds with a small smile as well.

Zelda closes the divider once again and puts out the candles after Link lowers the chandelier from the ceiling. She then walks over to her bed to sleep. Link had fallen asleep almost immediately, but Zelda had trouble doing the same; Link's last words ringing in her ears and making her anxious about his turmoil. Two hours pass and she had not fallen asleep yet. Fed up with this, Zelda sits up and looks at the Shiekah Slate and decides to occupy her mind with another subject; the machine human in the library.

"If it will help me find sleep again, I might as well give it a look." Zelda thinks to herself as she removes her white nightgown and puts on a blue-white tunic with yellow designs (omitting the gloves altogether), black pants, brown boots and tying her hair into a basic ponytail. She then quietly walks out of the room without waking Link and makes her way to the library, being extra quiet as the guest room, where Impa is sleeping in, is along the same path. Finally arriving at the entrance to the library, Zelda sees the two sentries have fallen asleep on their seats, much to her relief.

Zelda approaches the doors and begins opening them. "Don't creak, don't creak…." She silently says as she opens the door enough so that she squeeze through and slowly closes them, being careful to not make the handles click when they close.

"That was close, now then; let's check out our metal friend."

Zelda walks up to the still unconscious Samus, who is laid out on a table. Zelda begins writing down notes.

"Subject is a humanoid machine. Origin unknown; only known fact is that it came from the sky in a larger machine. Subject has a red head-like apparatus and chest, yellow lower abdomen and inner thighs and orange legs, outer thighs, oversized shoulders and left arm (side note: unknown device underneath said arm). Right arm is some sort of cannon; projectiles that it fires remain unknown for now." Zelda puts her journal down. "Now let's see if we can open you up."

Zelda looks around Samus's suit, but can't find any way of opening it. After a few minutes of not finding anything, she unintentionally strokes the left side of Samus's helmet, causing air to exit from underneath it and allow Zelda to see the silhouette of her face in it.

"I don't believe it. This isn't a machine at all; it's a person." Zelda says with quiet surprise. "Then, this is just a helmet. Time to see who you are, mister."

Zelda slowly removes the helmet and is left speechless by what she finds; an attractive young woman with mostly pale skin, blonde hair in a fairly long ponytail and a small beauty mark under the left side of her lower lip.

"My word….She's almost as tall as a Gerudo." Zelda puts the helmet down and updates her notes. "Addendum: subject is not a machine as previously thought. It is actually a, admittedly beautiful, woman in a rather complex suit of armor. This person is currently unconscious and will be monitored until she awakens." Zelda then picks the helmet up and decides to wear it. Unbeknownst to her, Samus begins to stir.

* * *

 **Back in the room, Link awakens from a small nightmare.**

"Ahh, stupid Lynels, why do you have to appear in my dreams?" Link says in an annoyed tone before lying back down. He turns his head to the side and notices that Zelda's bed is flat, indicating that she's not here. "Princess?" Link parts the divider and sees Zelda's nightgown on the bed, a drawer open with some clothes missing and the Shiekah Slate gone. Link realizes where she went. "Oh, Princess….." He says in with an exasperated mood as he puts on his boots and slings the Master Sword over his shoulder, exclaiming in discomfort as his wounds are still fresh before finally walking out. "Sometimes, this girl can be quite the handful…."

* * *

 **Back in the library**

"What does all this mean? HUD. Energy. Miss-ill capacity. I don't understand why this is written." Zelda says while wearing the helmet and commenting on the visors interior. She finally takes the helmet off. "Well, maybe you'll explain better when you wake-" Zelda turns around and sees that Samus is missing. "...up."

Zelda holds the helmet tightly and slowly walks toward the exit. Soon however, fast footsteps catch her attention. "Uh, Link? Was that you?" She asks nervously before walking in that direction towards the bookshelves. "Come on out, I just want to ask you some things. Are you from this land? Did the Goddess send you?" Zelda then gasps as the footsteps get closer and her eyes widen in fear. However, she relaxes as it was a cat that caused those footsteps. "Hah, don't scare me like that, little one. I thought you were-" Zelda stops abruptly as a cannon is pointed directly at the left side of her head. She moves her eyes to see the woman from before pointing her cannon at her.

"Don't move." Samus orders; her blue eyes flaring with seriousness.

"There is no need for that." Zelda answers nervously. "I just-"

"Shut up." Samus moves her cannon closer. "Give me that helmet."

"This?"

"NOW." Samus extends her hand.

"O-of course." Zelda slowly hands the helmet back to Samus. "It's yours after all."

Samus puts on her helmet and then moves in front of Zelda with her cannon still ready. "Hands where I can see them." Zelda complies and puts her hands up. "And where is my ship?"

"We don't have any ships. They were all destroyed a long time ago."

"I meant the one that I came in."

"That was a ship?" Zelda asks with bewilderment.

"Where is it? Tell me!"

Suddenly, Link pushes the door to the library open, with the added effect of waking the sleeping guards, and has an irritated look on his face. "Princess, I thought we agreed that this would wait until morning-" He stops suddenly to notice that Zelda is being threatened and draws his sword. "What is going on here?!"

"I could ask you all the same thing." Samus calmly answers.

"Get away from the princess!" Link orders as the one of the guards readies himself and the other runs off to wake the others. "Wait a minute, you're a machine; but you can talk?!"

"I'm a human. Mostly."

"Whatever! Lower your weapon now! We're taking you to the dungeon!"

Soon a squadron of Sheikah arrives and readies their weapons behind Link. Samus assesses the situation and decides to lower her cannon and then looks at Zelda. She nods her head towards the group, indicating Zelda to go with them. Zelda quickly walk off to the group and Samus speaks up.

"I'm not going to any dungeon." Samus switches to the light beam and shoots a fast shot of light into the air, causing a blinding flash. The entire group reels back to cover their eyes as Samus effortlessly jumps over them and runs through the halls to escape. Link recovers from the flash and tries to run after her. After running through several corridors Samus finds the entrance and hears the shouts from the group behind her and motions towards the closed gate. To everyone's shock, Samus jumps over the entire 30 foot gate and runs off into the rainy night.

"Lower the gate!" Link shouts after snapping back to reality and the guard complies in opening the gate. "Everyone stay here, I'm going after her." Link then runs off after her.

Zelda arrives 6 minutes later. "Get our horses! Now!"

"But your Highness, he told us to stay here." The guard comments to her.

"He's going to get himself killed! He's injured! Now I order you to bring our horses immediately!"

"I-As you wish." The guard gestures to two other Sheikah to retrieve Link and Zelda's personal horses; Soren (a white stallion with the royal saddle and bridle) and Epona (a chestnut brown mare with the same saddle and bridle). Zelda mounts Soren and guides Epona out of the gate and towards the field. "We'll be back soon!"

* * *

 **Central Hyrule field, by the sacred ground ruins, Link had managed to run all the way here before collapsing from exhaustion, his wounds continuing to plague him.**

"No...I can't let her get away…." Link says while dropped to one knee and breathing heavily.

"Link!" Zelda shouts from behind on her horse and reaches Link, she then dismounts and kneels down next to him. "Come on, we're returning to the castle."

"Not yet...She's still out there!"

"We can worry about her later! You're wounds haven't healed yet!"

"But…"

"She'll come back on her own, we have something she wants, remember?"

"That large machine?"

"Yes."

"Hah….Alright. Let's go back."

Zelda helps Link onto Epona's back and before they can go any further, an arrow hits Link on the shoulder, knocking him off Epona. Zelda shouts to Link in horror before kneeling to his side.

"Princess, look out!" Link screams as he grabs Zelda and rolls them both out of the path of a Yiga Blademaster's sword. Soon they are both surrounded by twelve other Yiga clan members.

"Who would have thought that both the princess and hero would be out here, ready for our blades?" The Yiga commander says. "Ganon is good to us; your deaths will be talked about for years to come."

"Ganon is gone!" Zelda shouts. "You have no more reason for this!"

"You're right; you made us lose our reason to fight, so now the hero is going to lose his. How does that sound, 'your majesty'?" He says while waving his sword in front of Zelda's face.

"Get away from her, you- argh!" Another Yiga knees Link in the abdomen, quieting him.

"You'll get your turn, don't you worry hero." The Yiga commander then prepares to run his sword through Zelda's stomach. "But first, I think you should watch her die"

At that moment, all of Links fears were made into light; as he knelt there, restrained by the Yiga, they planned to execute Zelda, the only one he had left in this world, in front of him. As Zelda shook in complete terror, Link couldn't stop looking at her eyes, as if he were saying, 'I failed you, again'. Tears began to leave Links eyes as he faced the inevitable.

"Goodbye princess." The commander readies to impale Zelda. In that instant, the commander's right arm is encased in ice and another shot shatters it. The commander drops to his knees and screams in pain as an orange flash drops from the dark sky into the center of the Yiga.

"I despise those who prey on the weak." Samus says in quiet anger.

"You…" Zelda says in shock.

"KILL HER!" The commander shouts in pained fury. The twelve other Yiga drop Link and Zelda and charge at Samus with their sickles and she fires her grapple beam (from under her left arm at one of them and swings him around, hitting the others. A blademaster gets up and tries to hit Samus with a wind blade, but she jumps over it, wraps her left arm around his neck, swings herself around, driving him down to the ground and blasts him in the face, killing him. She then engages the others with several power beam shots. Zelda rushes over to the injured Link and tries to get him up on his feet during the commotion.

"Link? Are you alright?"

"Yeah…" Link says half-heartedly before noticing the fight. "By the Goddess…."

Of the twelve Yiga that attacked them, eight have already been eliminated. Not wanting to risk anymore losses, the commander orders the remaining four to retreat. Before Samus could react, they all left in a flash of red lights.

"She beat them, incredible power….." Zelda comments.

"Just what are you?" Link adds.

Samus looks at the pair and then walks toward them, earning apprehension from them. "I think we got off on the wrong foot. Here." She says as she extends her hand and after a few seconds, Link accepts her help.

"Why did you help us?" Link asked.

"You're injured." Samus says as she scans his concealed injuries once again. "Attacking a wounded soldier is pathetic. Also, I should repay you with this for not attacking me while I was unconscious." She adds as Link and Zelda relax themselves.

"Thank you for saving our lives." Zelda says while bowing politely.

"Now then, you both should head back to your castle."

"Yes, we should. Oh, please come with us!" Zelda says with enthusiasm.

"That won't be necessary, thank you."

"We insist. Besides, your machine is there as well." Link replies.

"I had completely forgotten about it as I was leaving." Samus says embarrassingly.

"Please, it's the least we can do for your help tonight." Zelda says

"Hmm, alright. Thank you."

Zelda dresses Links new arrow wound and helps him onto his horse. She then gets on her own and they head back to the castle with Samus walking beside them.

"Oh, we haven't introduced ourselves yet; my name is Link and this is Zelda, princess of Hyrule." Link declares.

"It is a pleasure to meet you." Zelda politely says.

Samus looks at them both and smiles. "Nice to meet you, Link and Princess Zelda. I am Samus Aran."

* * *

 _To be continued_

 **Authors note: Whew, that took much longer than expected. Now, to anyone who might complain that this was a slow chapter, I felt that it was necessary to establish Link and Zelda's feelings after the calamity. As in they probably would be feeling the weight of the 100 years and all of the losses they've had to endure. Also, they really do have only each other now, so losing one would, in all likelihood, be absolutely devastating. I hope you all like this one and once again, rate and review please! :)**


	3. Chapter 3 Nightmare Revisited

**Chapter 3: Nightmare Revisited**

"When one with honeyed words but evil mind persuades the mob, great woes befall the state." -Euripides

Link, Zelda and Samus return to the castle to be greeted by several Shiekah that point their arrows at Samus, who Zelda stands in front of and orders them to stand down and that Samus is not their enemy, that she had saved both Link and herself from the dreaded Yiga. Link confirms her words and the Sheikah lower their weapons. Zelda then commands them to escort Link inside to check on his wounds. They then enter themselves and have a brief conversation.

"Now then, I feel that you owe us an explanation as well; where did you come from and why have you come here?" Zelda asks.

"Of course princess. I come from a distant place, millions of miles away from this world. I have come here because of an anomaly that I detected from here." Samus explains.

"An anomaly?"

"Yes, I detected it some time ago and it resembled an energy that I've encountered several times in the past."

"What kind of energy?"

"Well, I don't want to mention what kind it is until I can speak to you all at once. It would be best if you and others who hold higher ranks be present."

"I understand. You should know that our chief scientist, Purah, will be arriving this morning. Perhaps you could explain to her as well what this 'energy' is. For now, I feel that we should put this night behind us. Please, allow me to lead you to your temporary lodgings."

"Alright, thank you."

Zelda leads Samus down the hallways of the castle as many of the Shiekah look at her in curiosity, never having seen a 'warrior' like her before and trying to figure out exactly how Samus puts on the suit with no visible openings or creases. Soon, the pair reaches a moderately elegant room.

"We were going to use this room for ambassadors that would visit us, but you may use it for the time being." Zelda politely says.

"Thank you, may I ask what you will do now?"

"Link, myself and the rest of the guards should get some sleep before the morning arrives. I suggest you do the same."

Samus nods and starts making for the bed before being stopped by Zelda.

"Um…"

"What's the matter?"

"I was wondering...If you're not too busy tomorrow. Could you...maybe...tell me how your suit works?" Zelda excitedly finishes her sentence.

"...Excuse me?"

Little did Samus realize that she had unleashed Zelda's scholarly nature. "It's just that your suit doesn't seem like any regular suit of armor I've ever seen. It doesn't seem like you can just jump in or out of it. How do you breathe in it? How can you run so fast and jump so high? How can you shoot so many different kinds of magic from your right arm?"

"Princess." Samus raises her left hand to try and slow Zelda down, but she grabs her hand and continues her questions.

"What kind of metal is this?" Zelda asks while rubbing the armor. "I've never seen anything like it before. Your eyewear is green; does that mean you see the world through the color green when you wear your helmet?"

"Princess."

"There's also the question of your physicality. Do you have any bruises from your suit hitting you from time to time? If not, then how do you manage to prevent self-injuries?"

"PRINCESS!" Samus raises her voice.

"Yes?" Zelda meekly responds.

"I'd be more than happy to explain it to you. But do you think your questions can wait until tomorrow?"

"Oh...yes, that's fine too." Zelda says with her cheeks flushed. "Well, I'd best leave you to your business now. Good night, Samus."

"Good night, princess."

Zelda closes the door behind her and excitedly walks down the hallway, mumbling to herself that she should write down her questions so that she doesn't forget them. Back in the guest room, Samus sits on the bed, retracts her helmet and lets out a sigh, trying to get the idea of the energy signature out of her thoughts.

Back in the shared room, Zelda quietly walks in and sees Link sound asleep on his bed, having been escorted by the guards, the injuries still visible on him. Zelda lets out a small sigh and quietly berates him for being so reckless. She then closes the divider and changes back to her white nightgown before finally bringing the covers over herself and drifting off to sleep.

* * *

 **Meanwhile: The new Yiga clan hideout, 14 minutes after escaping their failed assassination attempt.**

The four surviving Yiga and the new commander, Silas (an older man with short grey hair and the regular Yiga attire), return to their hideout with several others waiting inside.

"Everybody, make way! The commander is injured!" One of the Yiga orders as they set Silas on a table to look over his severed arm.

"Who was that?! Where did that interloper come from?!" Silas shouts in anger.

"We don't know, but she was the most powerful warrior we've ever seen." One of the Yiga decides to speak up. "What do you want us to do, Silas?"

"I want her dead...I want the hero crucified and the princess dead at my feet! They will RUE the day that they defied us! The Yiga will not be so easily tossed aside as they had foolishly thought!"

The other Yiga grunt in approval. Silas, after having his dismembered arm bandaged, prepares new methods of trying to attack the castle, but soon they are interrupted by a cold wind emanating from all over the place. Silas stands up and orders the other Yiga to stay alert. Then, metallic footsteps are heard heading towards them.

"Who are you?! Show yourself!" Silas demands.

Out of the dark hallway, a dark blue and black armored figure appears, making some odd, otherworldly sounds.

"It's you! Attack!" Silas gives the order and several Yiga fire at the stranger, who takes all the arrows that then melt off of her body. She continues walking towards them and in response, they attack with their blades, only to be blocked by a force field she generates. Growing tired of their attacks, she generates a shockwave that knocks them all back and she swiftly approaches a stunned Silas.

"You're not the same person we met in the field….Who, or what, are you?"

She then begins to telepathically communicate with him, explaining very briefly who she is and why she is here.

"You come from another world? How did you arrive?"

The stranger responds in only one word: Leviathan. Silas continues questioning her motivations and the stranger answers in simple words. Finally, Silas asks his last question: "Why have you come to us?"

The stranger points her arm cannon at Silas and telepathically answers: "I am your new god…." She then fires a luminescent blue beam at Silas, causing him to fall over in pain as he is covered in blue, vein like tendrils. Soon, the pain subsides and Silas looks down in shock as his arm has regrown, although it is mostly a bioluminescent blue and black. The other Yiga recover and stare in awe. Silas flexes his new arm and marvels at the new power building up within him.

"Obey my rule….and you will rise again…" The stranger communicates.

"Heheh...Hahahah!" Silas laughs maniacally as he moves forward to address his followers. "Brothers! Sisters! Do not panic, for we have a new goal."

The members look on in confusion.

"Our objective is no longer Hyrule itself, but rather the whole world will be ours! With this new power, everything we've ever wanted will be ours for the taking. Our new god has blessed me with this, a power much greater than anything Ganon could have ever given us. Please, I ask you to show them, my liege.

The armored figure points to a random member of the Yiga and fires another shot at him. The member falls to the ground and convulses, the others back away in fear. After a while, his screaming subsides and notices that he feels more powerful. He excitedly proclaims that this new power is unlike anything that he'd ever seen and that the others should accept it willingly. One by one, the others apprehension begins to disappear.

"So now you see, brother. We need not fear this gift, we must embrace it!" Silas declares, earning scattered praise from the others. "We will follow her into this new path and the world will be cleansed with this new power: Phazon. And once this world is ours, many others after it will receive the same purification! We will triumph!" Silas raises his arms into the air, the phazon arching above him. "Are you with us?!"

The entire hideout erupts in applause and shouts of praise as the armored figure spreads the phazon to every Yiga present. Soon, all of them radiate phazon energy and are holding malicious, power-hungry smiles. Satisfied with this turn of events, Silas turns to the armored figure and bows to her.

"From this day, we shall carry forth your will. It is an honor to serve you, Dark Samus."

The other corrupted Yiga follow Silas lead and bow to Dark Samus, who in turn laughs ominously.

* * *

 **The morning after: Hyrule Castle.**

The thunderstorm has finally subsided; Zelda awakens to the sound of birds chirping. She gets up off the bed and walks over to the divider and sees that Link is no longer on his bed. Zelda concludes that Link has already woken up to continue their talk with Samus and is waiting in the dining room, as the meeting room is yet to be repaired. Zelda puts on her formal blue dress with golden designs and accents, white high neckline, midriff, lower dress and long fingerless gloves, after which she walks out and runs into Impa.

"Ah, good morning Impa."

"Good morning princess, what was all the commotion last night?" Impa asks.

Zelda remembers that Impa can sleep like a log, even if a pack of 20 Lynels were barreling through the land, she'd still be out like a light. Nevertheless, she explains to Impa about what happened last night: Samus (or the "machine human") waking up and running off, their run in with the Yiga and how Samus saved them.

"Goodness gracious. It's fortunate that our guest was very well versed in fighting. What did you say her name was?"

"Samus Aran."

"Well, I certainly owe her my thanks for keeping the two of you safe. Any ally of yours is an ally of the Sheikah."

Zelda giggles at this and continues walking with Impa towards the dining room. As they reach the dining room, Link is in fact waiting there, having made several baked apples for everyone.

"Good morning princess, good morning Impa." Link says with a smile, his wounds having mostly been healed.

"Good morning, Link." Zelda replies.

"Good morning lad, you're up bright and early. Color me surprised." Impa quips.

"I wanted to have everything ready for our talk. It needs to be just us, so I left the chef's sleeping, so they won't hear us, and I made this."

"You'll always jump at the opportunity to cook, won't you?" Zelda replies with a joking face. "Oh great hero of meals."

"Ha ha." Link sarcastically laughs. "Anyway, I had a guard tell Samus where we are, she should be here soon."

Sure enough, the doors open up and Samus walks through. However, instead of her varia suit, she is wearing a skin tight blue suit with light grey calves and an odd symbol on her left hand, chest and entire back. To be frank, they notice that Samus is lean and slender.

"Sorry I'm late, I- What is it?"

"It's just that this is the first time I've seen you without armor." Link answers.

"Yes, you're so...tall." Zelda adds.

"Oh honestly, you two. As if you've never seen an adult woman before." Impa interrupts. "Pay them no mind, dear. First of all, I am Impa, current chief of the Sheikah; it is a pleasure to meet you."

"The pleasure is all mine, Miss Impa."

"Now, I hear that you wished to speak to us?"

Samus confirms this and has all four of them sit down at the table. She starts off with telling them who she is: a human that was raised by the Chozo, an ancient race of bird people that infused her with their blood, granting her superhuman strength and reflexes. After giving a very brief history of her ascension to intergalactic bounty hunter, she explains the reason she came to Hyrule in the first place: she detected an energy signature that was very similar to phazon, a highly mutagenic compound that causes catastrophic changes in living organisms and even certain machinery. In addition, she explains in painstaking detail about several incidents involving the phazon (the space pirates, the Ing invasion of Aether, her own near corruption and Metroid Prime). After she concludes, Link, Zelda and Impa stay in complete silence over these revelations. Finally, Zelda speaks up.

"Unbelievable, how can such a monstrous thing exist?" Zelda asks in disbelief.

"It shouldn't anymore, because I destroyed the source of it some time ago." Samus answers with worry.

"So this phazon is some sort of plague?" Link asks.

"You could say that. Now that I recall, there is one thing that all victims with higher brain functions suffer from the corruption: psyche degeneration. All of them had an impulsive need to spread the phazon to any healthy lifeform."

"So, anyone can fall victim to this?" Impa questions.

"Yes."

The three try to process what Samus had just told them, the feeling of dread creeping its way into their hearts. All of a sudden, the doors swing open and Purah, accompanied by Symin, walks in.

"Well, I guess you guys forgot about our welcoming committee. That wasn't very hospitable!" Purah says with a pout.

Ah, Purah. I almost forgot that you were coming." Zelda stands up to greet the pair.

"Your highness, good to see you are well and in high spirits." Symin greets with politeness. "We've come to inspect-"

"Hey there Zellie, so how's the tin man? Any problems?" Purah cuts in.

Zelda gestures over to the table and Samus stands up to greet the new guests.

"Not exactly a tin man or even a man." Zelda comments.

Samus becomes confused at these turn of events. When she heard that the top scientist would be coming, she assumed that they would be an older man or woman. Instead, before her stands a child.

"You must be Purah, the princess has told me about you. She said you were the forerunner of science in this land."

"Aww, Zellie is just a big fan of mine, isn't she? Hee hee. But wait a minute; I thought you were a machine. No told me you were just a girl in a suit."

Samus raises an eyebrow at being labeled a "girl", but decides to humor her anyway. "Ah, you mean this?" The symbol on her back begins to glow, followed by the ones on her chest and left hand, and then various hexagons like particles spread around her, forming the varia suit. Leaving everyone present awestruck. "Princess, I believe I just answered one of your questions."

"I'll...be sure to write that down." Zelda answers with astonishment and Impa having the same reaction.

"So that's how she does it." Link says with a clearly impressed tone.

"Now then, shall I explain once more to our guests?" Samus asks Purah and Symin.

"Yeah...That would be great. Symin, be sure to write everything down. Ok?" Purah says in a dumbfounded tone.

"Snappity snap, Purah…" Symin responds with the same tone and picks up a journal. Thirty minutes later, Samus had brought them up to speed with what she explained earlier to the trio. While Symin was more concerned with what was explained about the phazon, Purah was more ecstatic about learning more about it. Concluding that her 'friend' would give them the final verdict on the energy signature, Samus has everyone present follow her to the ship. On a side note, Samus asks that if Purah is actually 200 years old, then why does she look like a six year old girl. Purah, Symin, Link, Zelda and Impa respond in unison: 'Long Story'. The group reaches Samus's gunship and she approaches it.

"Alright, time to wake up Virginia." Samus selects her command visor and reactivates the ships generator.

"You gave your 'ship' a name? I bet it can talk too." Purah quips.

"As a matter of fact I can, little girl." Virginia, the on board computer, responds. Earning a squeak of alarm from Purah.

"Who is speaking?" Zelda asks with surprise.

"Everyone, this is Virginia. My ships artificial intelligence or A.I." Samus explains. "Before anything else, Virginia, give me a status on the ship's condition."

"Hull integrity at 15%. Weapon systems at 78%. Shield generator fully functional. Power core at 63% and translator module active and fully functional." Virginia reports. "Auto repair in progress."

"Good, now I need- wait a minute, the translator module is active?" Samus questions.

"It has been active since you arrived; your suit activated it as soon as someone here spoke."

"Hmm, excuse me Link; can you recite a sentence for me?" Samus asks.

"A sentence? Like what?" Link asks with confusion.

"Anything at all. I want to test something." Samus says as she retracts her helmet.

Link complies and recites a passage from Hyrule's founding (which he knew by heart) and Samus removes the earpiece she had on. Sure enough, Link is now speaking in a language she's never heard of. Samus puts the earpiece back on and asks Link to stop. She then asks Zelda what language they speak and she answers with "Hylian". Samus was surprised by the fact that she was speaking to people that were not speaking a language similar to Terran. When Zelda ponders why she asked such an odd question, Samus dismissively replies that she'll explain later. Finally, Samus asks Virginia what the energy signature was and her worst fears are confirmed.

"Energy analysis complete. Source: Phazon." Virginia confirms and the group reel back in fear.

"It can't be. How is this possible?! I destroyed Phaaze (source of all phazon)." Samus inquires.

"I don't believe this. We escape one calamity and we face another one." Zelda remorsefully says. "This is terrible…."

"That explains the Guardian's sudden outburst." Link concludes. "If this phazons power does that, then what else could it be?"

"...Virginia, triangulate the source of the phazon in this planet." Samus quietly commands.

"Scanning….There is too much interference of unknown origin. Triangulation is impossible." Virginia states.

"Interference? What in the world is going on?"

"Samus, what is it?" Link asks with concern.

"I can't find the source, something is causing interference."

"Hmm, maybe we can use the Sheikah towers to find what you're looking for?" Purah comments. "We can use my lab to connect with the towers and scan the land, would that work?"

"It just might. Alright, we can head to your lab as soon as my ship repairs itself-" Samus is cut off as the castle begins to shake. Link grabs on to Zelda to keep her from falling as Symin does the same for both Impa and Purah. After a few seconds, the shaking subsides and Samus asks if everyone is alright. A moment later a guard runs in.

"Your Highness! Something has appeared in the land! I can't explain it!" The guard says in panic.

"Everyone! Get to the balcony!" Zelda shouts and they all run to the balcony of the dining room and they are shocked by what they find.

"What is all this…?" Link fearfully asks.

"Trouble…" Samus answers as she observes the massive luminescent blue barrier around the vast majority of Hyrule save for Central Hyrule and the Woodland Region. The phazon has begun its spread….

* * *

 _To be continued._

 **Authors Note: The story deepens…. Well, I finally got the next one up already. Now, the next one will be more development and the one after it will finally be some exploration. On another note, I made the part with Zelda asking Samus about her suit at the beginning funny because in one of the memories with Zelda trying to have Link taste a frog while explaining its properties (pretty fast at that) in BotW was one of the funniest things I've seen in a Zelda game. Also, to all the Metroid fans saying that Dark Samus died at the end of MP3: Corruption, remember that she can revive as long as there is phazon present anywhere. Well, stay tuned for the next one.**

 **Rate and Review please!**


	4. Chapter 4 The Next Step

**Chapter 4: The Next Step**

Alone we can do so little; together we can do so much. -Helen Keller

Using her speed booster, Samus runs around the outside of the barrier to do a quick check of how far it reaches. After an hour of running, Samus returns to the castle.

"What is the situation?" Zelda asks expectantly.

"Not good. The barrier covers most of the area, according to the map you gave me at least. If we try to walk through it, we'll either die or become corrupted." Samus reports.

"So what are we supposed to do?" Link asks in frustration.

"My ship has phazon shielding. But it won't fly until its back at 100% functionality. Virginia says that will take approximately 18 hours."

"So, until then, we're stuck here?" Zelda asks with concern.

"I'm afraid so…"

"Paya…" Impa mumbles to herself in worry.

"Don't worry Imps." Purah says reassuringly. "Paya is with everyone else in the village, she'll be just fine."

"Thank you, sister." Impa smiles at Purah.

"If I may." Symin speaks up. "In the meantime, maybe we could get the turrets up and running again? They might be helpful."

Zelda agrees and commissions both Symin and Purah to activate the turrets. Samus stops them and hands each one a scanner to check them for phazon corruption and any that show positive signs are to remain offline until Samus can purge the phazon from them (she has a phazon vaccine that she received from Aurora Unit 242). The pair head off to activate the turrets. Samus then turns to Link, who is on the balcony with a serious expression.

"Link? What is it?"

"It's so quiet out there. Something's wrong…" Link answers.

"Like what?" Samus asks.

Before anything else, Link takes aim at a Lynel trotting towards the castle. When it's in better view, they notice that it covered in blue splotches, indicating phazon corruption. It then stops several meters away from the castle and lets out a howling roar. Seconds later, the ground shakes and large, bioluminescent tentacles erupt from the ground and several bokoblins and moblins (all corrupted) emerge from within them and charge towards the castle.

"RAISE THE BRIDGE!" Link shouts to the guards. "DON'T LET THEM GET INSIDE!"

"Your highness, lady Impa, stay in here!" Samus orders. "I'm going out there!" Samus jumps out of the window, locks on to several enemies and then fires her seeker missiles, each one hitting their mark. The monsters begin to swarm her, but she activates her wave beam and fires several surges of electricity at the incoming bokoblins. A moblin flanks her and manages to strike her with its club, knocking Samus to the ground. Before it can strike again, an arrow strikes the moblin on its head, killing it. The attacker is revealed to be Link, who came down on his paraglider.

"Need a hand?" Link extends his arm towards Samus.

"You're always welcome to join in." Samus replies as she accepts Link's assistance. "Now, let's secure the area."

Link and Samus charge forward as the monsters run towards them with that same Lynel from before directing them from behind. Link uses his swordsmanship skills to lay waste to the attacking bokoblins while Samus uses her plasma beam to scorch the moblins. Samus yells out Links name as she kicks a bokoblin in the air and Link responds by attacking that same bokoblin. Back in the castle, Zelda commands the archers to fire at the enemies to assist the pair in their fight. After several minutes, one of the turrets shoots its laser at one of the five phazon tentacles, destroying it.

"Snappity snap! We got it!" Purah excitedly shouts. "Come on Symin, we need to get the others up and running. These turrets aren't at their best now, so we need a lot of them." Purah and Symin run to the next turret as Link and Samus continue their assault as that same Lynel joins in the fight. To their shock, it breathes a large, weapon grade, stream of fire at them, which they dodge. Samus concludes that this is a result of the phazon. Another shot is fired from a turret, destroying a second phazon tentacle and reducing the number of monsters.

"Just a bit more, we've got this!" Samus shouts as she fires her ice beam, freezing several opponents.

"I'm just getting warmed up!" Link drives his sword into the ground and conjures Urbosa's Fury, electrocuting several monsters and stunning the Lynel. Samus comments that Link has some of his own special tricks up his sleeve. She then shouts to Link while aiming at him and Link responds by holding up his shield as Samus fires her wavebuster at it, reflecting it around the field and hitting several enemies. Link applauds Samus as she gives him a thumbs up, but the Lynel recovers and tackles her.

"Samus!"

"I've got him; you just worry about the others!" Samus responds as she struggles to break free.

"Alright, don't you dare fail us!" Link continues his assault on the bokoblins rushing towards him. Zelda orders the archers to fire at the Lynel, but the target is too fast. As this is happening, another turret fires, destroying a third tentacle. Samus breaks free and maneuvers herself onto the Lynels back and aims it at the incoming arrows, hitting it several times. Zelda breathes a sigh of relief as the soldiers cheer. Meanwhile, Link has wiped out a third of the remaining forces; he then fires several bomb arrows at the moblins, causing them to fall on top of the bokoblins.

"The number keeps decreasing. It's just a matter of time!" Link shouts to the others.

"I hope so; this big guy is no pushover!" Samus responds as the Lynel tries to strike her with its crusher. As it tries to strike, Samus fires a super missile at its crusher, making it fall backwards. She then runs off to aid Link. The pair is now back to back.

"You still here?" Link quips.

"You wouldn't last too long without me." Samus jokingly responds.

"Come on, let's make the last push!" Link slashes diagonally at a moblin and slashes the bokoblins sequentially as Samus fires power beam shots at the incoming bokoblins. The archers continue shooting their arrows and Purah reaches the next turret and starts working to get it set up. After a few minutes, it shoots its laser and destroys the fourth tentacle. The Lynel, fed up with the situation, charges at the pair. Samus jumps to the side and aims at it, but is surprised to see Link rapidly slashing at it. Samus jumps in and does a mix of hitting it with charged shots and punches. Another shot is fired from a turret and the fifth and final tentacle is destroyed. The Lynel shoots an arrow up into the air and it falls to the ground, spreading phazon into the immediate vicinity (which Link and Samus avoid). Samus charges her speed booster and drop kicks the Lynel out of the phazon and lays a barrage of missiles at it. Mortally wounded, the Lynel lets out another roar as it lies on the ground. Link runs up and drives the Master Sword through its heart, finally killing it.

"Alright, let's finish off what's left of them and head back to the castle-" Link is cut off as another tentacle erupts from the ground and Virginia alerts the pair (from within Samus's suit).

"Samus, there is a large increase in phazon coming from that tentacle. Proceed with caution."

"Link, something is very different about this one." Samus alerts Link.

"Like what?" Link inquires as a large, three fingered fist erupts from it before finally revealing what it is: a large, humanoid creature with black armor and blue shoulders, two toed feet and a head with a spike on it. Zelda, Impa, Purah, Symin and the soldiers stare at the creature in fear.

"What in the name of Hylia is that?!" Link exclaims in shock.

"Virginia, confirm this." Samus commands as Virginia scans the beast.

"Scan complete. Morphology: Elite Pirate."

"What?!" Samus shouts in alarm. "Link, get out of the way!"

The Elite Pirate slams its fists into the ground and creates a shock wave that kills off the remaining bokoblins. Before this, Samus runs to Link, grabs him and jumps into the air to avoid the wave. Samus tells Link that they need to head back to the castle. Zelda tells Purah to aim the turret at the Elite Pirate. She complies and fires at it, but it swats the laser away with its fist. Samus fires another super missile at it, stunning the Elite Pirate. Link then runs towards the Lynels corpse and retrieves its quiver, explaining that it might come in handy later. The pair makes their way back to the castle with the recovered Elite Pirate in pursuit. Link stops momentarily and uses the stasis rune to freeze it in place, then he shouts at Purah to fire a turret while it's motionless. Purah has Symin charge the turret to maximum and fires the turret just as the Elite Pirate breaks free. The blast launches them towards the raised bridge, which Samus jumps over with Link. Zelda and the rest run downstairs to check on them.

"Link! Samus! Are you both alright?!" Zelda asks with concern.

"We're fine. A little shaken, but fine." Link says as Samus give the thumbs up.

"What in the world was that thing?" Impa asks.

"Something I didn't think I'd ever see again." Samus replies.

Their chat is interrupted as loud banging is heard from the raised bridge. The injured Elite Pirate climbs up it and jumps into the courtyard where they are.

"Everyone, get back!" Samus shouts as she fires on the attacking Elite Pirate. Link has Zelda and the others return to the castle interior before engaging it. The Elite Pirate fires several laser shots at the pair from what appears to be a modified guardian turret on its right shoulder. Link shoots an electric arrow at its head, temporarily stunning it and giving him time to lay flurry of slashes at its compromised armor. It recovers and tries to slash at Link with its bayonets (its fingers that elongate and become bright blue), which he blocks with his shield, sending him back a few inches. Samus follows up by charging a shot and "punching" it into the Elite Pirates face, breaking the armor on its upper body. Angered, it drives Samus into the ground with its bayonet and she desperately tries to keep it from impaling her. Link jumps up to help her, but it grabs and holds him aloft. At that moment, Zelda runs out and uses her power to keep it from moving, causing it to roar in anger.

"Link, now's your chance! Destroy it!"

"Link, don't worry about me! Take your shot!" Samus shouts as Link escapes the Elite Pirates grasp and jumps up into the air.

"HYAAAAHHH!" Link slashes at the Elite Pirates neck, decapitating it. The bayonet deactivates and Samus moves out of the way before it falls on her. With the crisis finally averted, Link goes to check on everybody.

"Princess, that was very reckless of you. You could have been hurt." Link says with seriousness.

"But I couldn't let that thing kill you-" Zelda explains before being cut off by Link.

"Exactly, without your help, we probably wouldn't even be speaking now. Thank you." Link smiles at Zelda and she blushes.

"Yes, I am indebted to you, Princess." Samus extends her hand and Zelda reaches out to grab it. "Thank you for your help."

"Thank you, for being on our side." Zelda responds.

"Well, this is all very touching." Purah walks out, covered in smoke from the turrets. "But, there is still another matter to discuss; what was that thing?" Purah points to the disintegrating Elite Pirate.

Samus explains that it was a creature known as an Elite Pirate, a monstrous creature that was artificially created by infusing phazon with a space pirate embryo that was to be used as a bioweapon of an experiment the space pirates conducted called "Project Helix". Samus had previously destroyed all the research involving it, so she doesn't understand why one of them appeared here of all places.

"Unbelievable, how can someone do something so abhorrent?" Symin questions.

"Their quest for power knows no bounds." Samus answers directly. "Come on, let me take look at those turrets that weren't activated."

* * *

 **Meanwhile, at the Yiga clan hideout.**

"My liege, forgive me for questioning you, but what was the point of sending a squadron of monsters and an Elite Pirate to storm the castle instead of us?" Silas calmly asks and Dark Samus responds telepathically: Test of strength. She then asks him if he has "what she wanted".

"Yes, I personally saw everything there." Silas answers and Dark Samus looks into his memories. She sees the strength that Link is capable of, as well as his prowess with a sword. Her curiosity turns to anger as she sees Samus fighting alongside him. She remembers all the misfortune that Samus had brought in their previous encounters and begins radiating phazon out of anger.

"My liege, we will slaughter this intruder, be certain of that." Silas declares after witnessing Dark Samus's reaction. "Now, we must make preparations for Zora's Domain and Kakariko village once your creatures do away with everything there. If you'll excuse me." Silas bows and then walks away.

From the shadows, an unknown voice speaks to Dark Samus.

"At least your new slaves are tenacious; I thought they'd be less willing to join you." The voice says as Dark Samus responds: "Revenge consumes them."

"Heheheh….That's one thing we have in common. I wonder how they'll fare against Samus, even with the data from Project Helix I provided you with; can they exceed your expectations?"

"We'll see…"

"I suppose we will." The voice leaves and Dark Samus looks at a room filled with strange eggs that have already been hatched.

* * *

 **Later that night, Hyrule Castle.**

Samus had spent most of the day infusing the guardian turrets with a "phazon vaccine" program to keep them from being corrupted. Link and Zelda, along with Impa, Purah and Symin discussed their next course of action, concluding that they should head for the Dueling Peaks and Lanayru regions first. Impa in particular wanting to secure Kakariko village and to know about the safety of its inhabitants. While this is going on, Samus walks up to the stables to admire the horses, now that she had some time to spare until the ship finishes its repairs. Apart from Epona and Soren (Zelda's white stallion), a large black horse with a red-orange mane catches her attention. She goes to stroke its mane and it knickers in comfort.

"He's a nice horse, isn't he?" Link speaks from behind.

"Oh, hello Link. I was just looking at the horses. It's been a while since I've seen one." Samus comments while petting the horse.

"His name is Strife. He's supposedly the last of his kind. I didn't want to believe it, so I wanted to look for a female to try and breed him, but with everything going on, I didn't have the time."

"Breed him?"

"I don't like the idea of his kind just dying out. I'd like for it to continue."

"Well, that would be a worthwhile endeavor. I hope you succeed in doing so." Samus responds with a somewhat sad expression.

"Is something wrong?"

"Hmm? Oh no, I'm just exhausted from today. I better go and check on my ship before turning in. I'll see you tomorrow."

"Alright, goodnight Samus."

"Goodnight Link."

Samus leaves the stable and heads down the hallways of the castle. Upon reaching Zelda's study, she sees her sitting at her desk while looking at an old picture. On closer inspection, she sees both Zelda and a man with royal clothing, concluding that it is the king, in other words, her father. Zelda's eyes begin to swell with tears and Samus remembers how she was told that during the "calamity", her father was killed and she had no choice but to escape the castle with Link. Instead of having Zelda see her, Samus walks off to let her have some privacy, commenting to herself that the two of them aren't so different. She finally reaches the ballroom where the ship is and asks for a status report.

"Hull integrity at 79% and power core at 92%." Virginia reports.

"Good. And how is the "item" doing?" Samus inquires.

"Preparation is going smoothly. Estimated completion time is 4 hours."

"Excellent. Virginia, I leave everything to you."

"There is no need for any concern. Sleep well Samus."

Samus heads for her room and closes the door behind her. Upon entering, she feels a presence and quickly activates her suit before aiming at its direction.

"Who's there? Come out now!" Samus orders as a man appears out of thin air, surrounded by green, ethereal lights.

"Do not fear, Samus. I mean you no harm." The man speaks before introducing himself. "I am Rhoam Bosphoramus Hyrule, the last king of Hyrule."

"King? Then, you're the father of princess Zelda?" Samus asks after lowering her cannon.

"Yes. As the king, I thank you for saving the princess from the clutches of the Yiga. But, as a father, I am eternally grateful to you for saving my daughter and her appointed knight from certain death. Even now, with this new threat to them. I cannot thank you enough."

"I appreciate your kind words, but I don't understand; how are you here, I was told that you were…"

"You are correct; I am no longer part of this world. The great goddess Hylia has granted me the time to return to this world, so that I may relay my knowledge to you. Please, sit.

Samus complies and sits on her bed and king Rhoam details to her what he knows.

"Long before you arrived, during the great calamity, a massive object came from the sky and impacted the land. As I awaited for Zelda's appointed knight, Link, to awaken from his century long slumber, I searched the area where it crashed. But I found no trace of it. Even after an entire century, it never appeared nor shown any signs of damage, until two days ago."

"What happened two days ago?" Samus asked with genuine curiosity and dread

"It began to stir, something creeped forth from within it. In a word: evil."

"The phazon." Samus concluded. "If I'm not mistaken, that object was a leviathan seed."

"You know of this evil, I presume?"

"More than I care to admit… Where is the seed?"

"I cannot say for certain, all I know is that it is somewhere deep underground."

"But why did this seed awaken, after all this time?"

"I would conclude that it had to do with Calamity Ganon's influence over the land. After Link and Zelda destroyed that scourge, its influence disappeared and allowed it to awaken after festering for so long. Now, they face a new calamity…. Please, accept this father's request; use your knowledge of this evil and aid my daughter and her knight in this time of darkness."

"I have heard your plight, king of Hyrule. I will help them to destroy this blight on their home. You can count on me."

"Thank you. I will be watching over you."

"Wait your highness. Don't you think you should speak to the princess? I think she would like to see you again."

"When the crisis has passed, I will tell her everything I need to say. I entrust this to you, Samus." King Rhoam concludes before finally disappearing, leaving Samus to process what just transpired.

* * *

 **The morning after.**

Samus awakens bright and early to prepare her ship, which she had moved to the front of the castle. Link, Zelda and the others arrive soon after. Zelda, having opted to wear the same clothing she wore when she first met Samus and Link wearing his champion's tunic and hylian trousers, approach the ship.

"I'm not going to lie; this machine looks a lot better than I thought it would." Link comments while admiring the ships appearance.

"It looks like your helmet, are you trying to the others that you're on your way by letting them see your head flying towards them? Hoo hoo!" Purah exclaims with excitement while Impa and Symin shake their heads in embarrassment.

"Can it seat all of us?" Zelda asks.

"Oh definitely, however, Purah may need to sit on someone's lap. I don't have baby seats." Samus comments, earning an annoyed 'hey!' from Purah and scattered laughter from the others, much to Purah's frustration. "Oh yes, Link, I have something for you."

"Me? What is it?" Link curiously asks.

"I see that you have the talent for fighting and spectacular reflexes." Samus pulls out a device from her ship. "I think this will serve you well, put it on. Remove your weapons first."

Samus hands Link a badge like object, with the triforce-loftwing symbol on it, which he places on his chest. In that instant, it glows and spreads hexagon-like particles all over his body, shaping a form fitting suit in the style of his tunic and trousers, having a metallic aspect to it. Along with a helmet shaped like a black hood with a visor, which retracts down.

"What is this?"

"It's a suit I designed for your use. It allows enhanced maneuverability and freer movement. It also uses kinetic energy, that is movement, to enhance your overall strength. The neural interface allows you to perceive your surroundings even more accurately; you'll be able to attack several enemies at once before they know what hit them."

"Wow, it feels so light…" Link comments while stretching his arms.

"I also added some extra features to it; I'll explain them on the way. For now we should head to our destination. I'll give you some time to get ready." Samus enters the ship from the top.

"Well, how do I look?" Link asks and Impa, Purah and Symin express their opinion, mostly impressed by what they heard it does. Zelda only looks at how much the suit accentuates his physique, causing her to blush. "Princess, are you alright?"

"Oh! Yes! I-I mean, you look fine. Fit for battle. Now then, let's get inside the ship, shall we?" Zelda quickly walks under the ship and stands in the small lift to send her up into it. After she leaves, Purah breaks out into laughter, much to Links confusion. After a few seconds, the others board the ship.

"Are you comfortable, Purah?" Zelda jokingly asks Purah, who is sitting on her lap.

"Shut up, Zellie….." Purah responds in embarrassment, causing Impa and Symin to chuckle.

"Alright everyone, our first stop is Kakariko village. We'll assess the situation and check on the villagers, after that we'll make our way to Hateno village to drop off Purah and Symin at their lab so that they can be our contact from this 'Shiekah slate' device. From there, we'll plan our next step. Any questions?" Samus asks the group as she powers up her ship.

"What does the phazon look like?" Link finally asks.

"It's bright blue and luminescent, your suit will react when it's close by. Remember; do not touch it under any circumstance. Now, let's get going. Everybody hang on."

The ship rises up into the air, activates a transparent layer around it (the shield) and flies through the barrier, into the phazon infested land.

 _To be continued_

 **Authors Note: What?! I'm hurrying with the releases?! …Huh, who knew? I decided to give Link an upgrade because, needless to say, there are going to be some really big threats than he's already used to. Next chapter will be in Kakariko, Hateno and, hopefully, certain parts of Lanayru. Stay tuned!**

 **Once again, rate and review please!**


	5. Chapter 5 Calm before the storm

**Chapter 5: Calm before the storm**

"A sure friend is known when in difficulty" -Quintus Ennius

 **Link, in his new suit, walks into an unknown area with metallic walls and ramps. As he walks closer, a small machine drops down and blares an alarm before returning to the ceiling. Soon, the doors open and a squad of space pirates (16 in total) run out to face him. One of them tries to hit him with its energy scythe, but he parries it and follows up with a swift horizontal slash, killing it instantly. Another three fire energy beams at him, which he effortlessly dodges and shoots three arrows at once, each hitting their mark. As the three enemies fall to the ground, another tries to blindside Link but, using his advanced perception, he jumps out of the way, move behind the pirate and slashes downward. Another pair run towards him and he parries the attack and slashes the first one before following up on the second one with an upward stab. Link grabs his bow and tightens his grip on its handle, causing energy to surge in it. He then nocks an arrow and sends it flying, hitting a pirate that was 20 feet away. He repeats the process, but he waits until the next three line up in his sight. When they finally do, he shoots the arrow, penetrating their heads sequentially. The final enemies surround Link and he holds his sword in front of him as he prepares himself. They all charge with their scythes and Link spins the sword, parrying all the attacks. He follows up with a lethal slash on one and chains the same attack on the others, with the feeling that time slowed down. After he concludes, the pirates let out a collective dying roar before falling to the ground. Link swings the blood off of his sword and finally sheathes it. A voice then speaks to him.**

" **Virtual Reality Training complete. Training time elapsed: 47 minutes, 38 seconds."**

Link awakens on the ship and removes the cable connected to the back of his helmet, which then retracts.

"Welcome back to reality." Samus says while flying the ship.

"It felt real…"

"That's the idea of 'virtual reality'. Did you get a good feel of the suits capabilities?"

"Yeah, it's impressive."

"You were out like a light, Linky." Purah comments. "Just 4 minutes though."

"4 minutes? I thought it was longer."

"The time in VR moves faster, that's why it felt like you were there longer." Samus explains, earning a surprised expression from Link. "Now, we should be arriving at the village soon." Suddenly, Virginia interrupts the conversation.

"Samus, there are several phazon signatures emanating from the village, each one on a mobile source."

"Understood. Link, get ready to put that suit to the test."

"You don't even need to ask." Link says while re-equipping his helmet.

* * *

 **Meanwhile, the Yiga have started an attack on Kakariko village. The Sheikah put up a great resistance, but the new power of the Yiga has made the fight even more difficult than they thought. Among the combatants is Dorian, an older Sheikah and one of the two guards of Impa's residence, who gives out the orders to the other Sheikah.**

"Hold them off! Do not let them enter Chief Impa's residence; we must protect lady Paya!" Dorian orders as he faces a Yiga swordmaster, his eightfold blade breaking from the impact of his enemy's windcleaver blade. Fortunately, Cado, the 2nd guard appears and parries the attack as Dorian brandishes his ancient short sword, an orange sword with intricate symbols and a bright blue energy blade, and impales that same Yiga through the chest.

"Cado! Get the elderly inside; I'll hold them off!" Dorian shouts as he removes his sword from the Yigas corpse. Several other Sheikah join the fight and Dorian spreads them out. "Fight for our home!"

"Traitor!"

Dorian turns around and sees a Yiga footsoldier toss away his duplex bow and pulls out his sickle. Dorian prepares to engage him, but is shocked when the Yiga glows blue with tendrils emanating from him and his sickle extending to an almost whip like appearance. The Yiga charges as Dorian blocks the incoming attack, staggering from the sheer strength of it. Dorian does his best to fight back, but is distracted by the screams of his children.

"Daddy!" Koko, one of Dorians daughters screams as she and her sister, Cottla, are restrained by another Yiga. Dorian turns around to face them.

"How dare you?! Release my children!" Dorian rushes towards them and the footsoldier he was facing takes advantage of the situation and swings his phazon whip, sending Dorian flying to a nearby wall. He is then restrained by the same Yiga as he prepares to deal the finishing blow as Koko and Cottla scream for their father. At that moment, a blast of energy hits the phazon powered Yiga, killing him. The Shiekah and the Yiga look up and see Samus's ship flying towards the village and then hovering above it.

"Nice shot." Link comments.

"Now then; go get them, hero." Samus says as she opens the top hatch of the ship so Link can jump down.

"Alright, you four stay up here; I'm going down there."

"Be careful Link, something is wrong with the Yiga." Zelda warns Link before he heads down.

"I'll be careful, don't worry." Link jumps to the top hatch and glides down to the ground. Before landing, he shoots an arrow at the Yiga restraining the children, killing him and allowing the two to run into their fathers' arms.

"Who are you?" Dorian asks.

"An old friend." Link retracts his helmet and smiles.

"Link!" Koko shouts excitedly.

"You're back!" Cottla beams in happiness.

"What is going on? Why have the Yiga grown in power?"

"I'll explain later. For now, we need to secure the village. Is there any place the kids can hide?"

"I know a place, wait a minute; Claree!"

"What's the problem?" Claree, a young Sheikah woman and owner of the village boutique, approaches the pair with her bow ready.

"Get the children and the elderly inside; we'll drive off the Yiga!"

"Got it!" Dorian then hands his daughters over to Claree, who then rushes them into her boutique before heading off to find the elders.

"Now, let's get these guys." Link draws the Master Sword and points it at the attacking Yiga. Dorian rallies several Sheikah to join the fight. Samus prepares to join the fight.

"Autopilot engaged." Virginia states as the top hatch opens up.

"You four wait here, I'll send the ship down when it's all clear." Samus explains before jumping up and somersaulting down, her body radiating an orange-red energy and landing on a pair of Yiga soldiers, obliterating them. Dorian asks who she is and Link responds that she's a friend. Samus fires at several Yiga trying to attack unarmed villagers while Link and Dorian fight off three phazon powered Yiga, which Samus makes a note of for later. Unfortunately, two footsoldiers bypass the trio and make it up to Impa's house where Paya, Impa's granddaughter, is being hidden, earning alarm from both Dorian and Cado.

"I'll handle it, you two worry about those guys!" Link shouts as he runs towards Impa's house, but stops as both Yiga are tossed out from the front door. Paya then walks out with a serious expression and holding an ancient spear, a spear with intricate orange designs and a triple spearhead made out of blue energy.

"Leave our home; now." Paya commands as she threateningly points her spear at them. The two footsoldiers rush her and Paya somersaults over them and hits both their heads with the blunt side of her spear, causing them to stagger. "This is your final warning…"

The pair recovers and charge at Paya once again. Paya, using her new spearmanship skills, blocks their attacks with little to no effort. She then parries one of the footsoldiers, rapidly stabs him in the abdomen and then swings the spear across his head. The other Yiga slashes vertically and Paya swings the spear horizontally, throwing his sickle to the side and leaving him open to a thrust from her spear.

"I guess you didn't need my help after all." Link quips while being clearly impressed.

"Who are you? Why are you here?" Paya asks with seriousness.

"Paya, it's me." Link retracts his helmet, causing Paya to go from serious to flustered, as well as dropping her spear.

"M-m-master Link! It's g-great to see you again! I'm s-sorry for n-not recognizing you…"

"Hahah, no problem. I almost didn't recognize you with the way you fought."

"Ahh! W-was I really t-that impressive?"

"Of course. I'm proud of you-"

"Link!" Samus shouts while helping several Sheikah fight empowered Yiga footsoldiers. "Am I interrupting?!"

"We'll talk later, I've got to help. Be careful!" Link runs toward the others. Paya picks up her spear and decides to do the same. Before Link moves any further, he sees Dark Samus staring at him from atop one of the cliffs surrounding the village and before he can react, she flies away. Link wonders who that was and why she almost resembled Samus. Ten minutes later, they manage to drive off the remaining Yiga and the Sheikah cheer.

"The village is secure; I'm not picking up any more phazon signatures." Samus comments.

"I thought it wasn't going to stop." Link says with exhaustion.

"Virginia, bring it down." Samus gives the command to Virginia to bring the ship down. It lands in the center of the village (which is clear of people).

"Hold on, just who are you and what is this thing?" Dorian asks.

"My name is Samus Aran. I've come to help you. In fact, she can vouch for me." The bottom hatch of the ship lowers and Impa steps out of it.

"Grandmother!" Paya excitedly runs up to Impa and hugs her.

"Oh my dear, I'm so glad you are unharmed." Impa comments as she returns the hug. "All of you as well, you fought valiantly. Our village is safe once again."

The entire village erupts in applause, several of the villagers rush over to thank Link for his aid, Koko and Cottla gleefully run to their father and Paya stays by Impa's side. The cheering stops as Zelda descends from the ship and all of the villagers bow in respect. She is soon followed by both Purah and Symin.

"Huh, now this is more like it!" Purah happily comments.

"Purah, I believe they are bowing for the princess." Symin interjects.

"Sheesh, way to kill the mood, Symin."

"Now now, we have much to discuss. Your highness, if you would be so kind." Impa speaks up.

"Thank you, Impa." Zelda kindly says. "All of you please rise. Now, first of all, Hyrule is not the only one in danger; but rather our entire world is at risk of extinction." The villagers reel back in shock at this announcement. "This barrier over the land is the cause of a starborne blight that has plagued several worlds before ours. If we do not stop this, then all will be lost. But, a new hope has come from the stars as well; in the form of our new ally." Zelda extends her arm over to Samus and beckons her to come closer.

"As I said before, my name is Samus Aran; I come from a world far away from this one. I have faced this evil many times in the past and I will aid you in this fight as well. I will pass on my knowledge of it to all of you, so that you may know what you're up against."

"I understand if you have some suspicions of her, but understand that she can be trusted." Link interjects. "Just as she did for all of you, she saved the princess and myself from the Yiga and their new leader. Without her, we probably wouldn't be here speaking." The villagers then nod their heads slightly at Samus, indicating trust.

"So now you know; with our alliance, we will purge this evil from our home. Just as we did for the calamity. We will prevail." Zelda declares proudly as the villagers applaud.

* * *

 **Later that night, Purah and Symin had spent the remainder of the day fixing the guardian turrets at the entrances to the village as well as purging any phazon from the small guardian scouts that were brought earlier to the village. After several hours of consulting with Impa, the trio decides to take the rest of the night to relax and prepare for the next morning. On another note, out of gratitude for saving the village, Koko had prepared meals for all five of the visitors (Samus in particular being intrigued by the idea of mixing meat with pumpkins). The five were then given fold out beds inside Impa's house, which Zelda has already fallen asleep.**

"She's out like a light." Samus, wearing her zero suit, commented to Link, who was still awake and had deactivated his suit.

"Today was a big day after all, I'm glad she's sleeping soundly." Link responds. "She's been having nightmares lately. All of them about the calamity."

"Everyone has mentioned this calamity several times, what exactly happened?"

Link, not having any objections, tells Samus about what happened long before she arrived. A monstrous evil known as Calamity Ganon wreaked havoc over the land of Hyrule. The people had ancient machines called guardians and four massive contraptions known as the divine beasts to combat this threat. Their best chance at winning was Zelda, who had a sealing power locked away within her that could defeat Calamity Ganon, but she unfortunately could not unlock it in time; the calamity rose again and laid waste to everything and everyone. Despite their best efforts, Calamity Ganon took control of the guardians and the divine beasts and Hyrule fell in a matter of minutes, among the casualties were King Rhoam and the four champions: Mipha of the Zoras, Revali of the Rito, Urbosa of the Gerudo and Daruk of the Gorons. While escaping from the attacking guardians, Link was gravely injured protecting Zelda and held his last stand to protect her. At that moment, Zelda awakened her sealing power and banished the malice from the guardians. However, the fight took its toll on Link and he collapsed to the ground. Zelda desperately pleaded for Link to stay alive, but he lost consciousness. The next thing he knew, he woke up in a strange chamber with next to no memories. Samus listened to every detail of the account, asking an occasional question, and at the end of it, she spoke up.

"So, you've been asleep in that chamber for the past century?" Link nods to answer Samus's question. "What happened after that?"

"The spirit of the king told me to save the princess, who was trapped in the castle trying to keep Ganon from escaping. I first went to free the divine beasts and the spirits of the champions, they helped me to defeat that thing that killed them. Finally, with the help of the princess, I finished what Calamity Ganon started and she sealed it away for good."

Samus listened in silence and she realized that they had been through so much recently and now a new threat looms over them. "Well, at least it can't hurt anyone else ever again and you kept your word to the king by saving the princess."

"And I will keep protecting her." Link stares silently at the peacefully sleeping Zelda. "She's all I have left."

"You have a lot of love for her, don't you?" Samus smiles kindly.

"D-don't misunderstand; I'm her appointed knight, it's my duty to protect her." Link says while flustered.

"Uh-huh." Samus quips.

"What's that supposed to mean-?"

"Link, good thing you're awake, can you come with me please?" Impa walks down the stairs and asks Link to accompany her to the balcony, which he nods at. Before leaving, he tells Samus about a blue armored figure that almost resembled her that he saw, to which Samus could not believe as true, but thanks him for telling her (all the while contemplating if that person that Link saw was truly the same one she was thinking of).

* * *

 **Out on the balcony.**

"Well, I see Paya has learned how to fight in these past two months." Link comments.

"She's been training daily since you went to save the princess. You've become an inspiration for many of us and Paya is no exception." Impa proudly says. "But that is not why I have asked you out here; I know that there is the issue with this phazon and that it takes precedence over all, but the status of Zelda needs to be taken in to account, especially if we are to unify the land once again. You know what I mean, don't you?"

It took Link several seconds to understand what Impa is talking about, but he realizes what she was getting at. In fact, it was a subject that Zelda had been avoiding for a while now; her coronation.

"Oh, you mean _that_."

"Yes, I decided to leave it in the air for a while, she was exhausted from her stasis in containing the calamity and she did not need any more worries, but even after 12 days she has not spoken on the subject at all."

"What do you want me to do?"

"For now, stay focused on the task at hand. But keep in mind that you should speak to her on this subject whenever you get the chance. Hyrule needs its queen, you know that."

"I will do what I can. Just give me more time." Link reluctantly answers.

Impa concedes and the pair reenters the house. Purah and Symin appear a few moments later, both exhausted from the repairs to the turrets and scouts that they don't even acknowledge that Link and Impa were in front of the door and push the pair aside, much to their confusion.

* * *

 **The morning after**

The group (except for Impa, who is staying behind to run the village) prepares to enter the ship to head for Hateno village. Impa wishes them well and hopes for their success in this time of uncertainty and Paya promises that the village will be safe and that she has faith in all of them. Zelda gives one more hug to Impa and prays that everyone be safe before entering the ship. Paya walks over to Link and whispers in his ear, to which Link smiles at. Purah and Symin enter after activating the turrets and both wave goodbye to the villagers. The ship rises to the sky and takes off towards the east as the villagers cheer to wish them well.

"Are you sure you didn't want to go with them, Paya?" Impa asks.

"I'm sure grandmother; I am needed here." Paya answers. "If the Yiga come back, we'll need to be ready for them."

"Hmm, I agree with you. But it seemed like you wanted to aid them on their quest."

"I would just be in the way; they need to focus solely on this task and nothing else, especially Link."

"Ho hoh, is that what you told him before he left?"

"Actually, I told him that the princess needs him and that he should take care of her. I know he'll keep his word." Paya smiles at this.

"Ah, my dear, you've certainly grown up quite a bit. But, I'm glad you're still my little papaya seed."

"G-grandmother, please don't bring that up again. I'm fortunate that our new friend and the princess didn't hear that…" Paya says with red cheeks.

"Oh, they know already; I told them at dinner when I showed them paintings of you as a baby. They thought your birthmark was really cute." Impa comments as she walks back into her house. Paya remains motionless and seconds later, her eyes widen and her entire face turns beet red.

"GRANDMOTHER!" Paya shouts in mortification.

* * *

 **In Samus's gunship heading towards Hateno village.**

"I see Robbie has been keeping busy; did you see all the ancient weapons the villagers had?" Purah comments.

"Oh, that was me." Zelda speaks up. "I paid Robbie to supply them with ancient weaponry to better defend their village. I thought that, during the siege of the castle, looters would come by and steal from the treasure chamber, but thankfully no one ever did."

"And you went to Robbie for a big shopping spree." Purah quips.

"Hee hee, you could say that."

Meanwhile, Samus asks Link about the fact that she overheard the Yiga label Dorian a 'traitor' and wonders what they meant. Link explains that Dorian used to be one of them and upon meeting the woman who would become his wife, he defected. Sadly, she paid the price for his desertion when the Yiga appeared and executed her, sometime after their children were born. Since then, he has lived every day making sure that no harm would ever befall his children or the village. Samus becomes appalled by the cruelty of the Yiga and remains silent throughout the remainder of the flight.

* * *

 **After 11 minutes, they reach the entrance to Hateno village, which Link had asked to be dropped off at so that he can explain to the concerned villagers about the phazon barrier over the land and that he'll meet them at Purah's lab. The others reach the lab and Purah tries to communicate with the other Sheikah towers.**

"So, what's the news?" Samus asks.

"Hmm, not good. I can only link up the Dueling Peaks, Hateno and Lanayru towers. But with the barrier, I can't even communicate outside." Purah answers

"This is quite the predicament, what should we do now?" Symin adds.

Just then, Link walks in. He managed to quell the people's doubts and he brought some provisions.

"Link, we have some bad news; the barrier is jamming communication with the towers, so we can't find this 'leviathan' object." Zelda comments.

"Great." Link sulks. "So, what's the next plan?"

"Well, we can try finding the source of the barrier and-"

Samus is interrupted as the doors swing open and a Zora wearing royal ornaments and covered with injuries falls on the floor.

"What in the world?!" Zelda exclaims.

"Sidon?!" Link yells before kneeling down. "What happened to you? What did this?"

"Link? Heheh...good to see you again." Sidon, revealed to be the crown prince of the Zoras, weakly comments. "How ironic that I find you, when I need help again."

"Good heavens! Did the Yiga do this to you?" Symin asks with concern.

"No, it was not the Yiga; it was a monster. It took four of our warriors to take one down, but they just kept coming. I was the only one who survived, but we managed to evacuate my people. I've never seen anything like them."

"What did they look like?" Purah asks.

"Some looked like giant insects; others looked like bipedal lizards; like lizalfos, only bigger and much more aggressive. But, if I could give a better description, the smaller ones looked like flying jellyfish."

"Flying jellyfish?" The rest repeat in unison.

"You." Sidon gestures at Samus to come closer. "The rumors are true; the armored spellcaster."

"Me? What do you know about me?"

"I know you helped the princess and Link a few nights ago. I know that you are not here for nefarious purposes. Therefore, please; help us…" Sidon asks before losing consciousness.

"Sidon!" Link yells in panic.

"It's alright Link, he's just unconscious." Zelda confirms.

"Symin, get the kit!" Purah orders Symin, who complies and runs to get the first aid kit.

"What creature was he talking about?" Link asks.

"I have an idea; I just pray I'm wrong." Samus says as she checks the status of her ice beam.

"Well, we know what to do next; we need to head for Zora's Domain. Now." Link says as he helps Sidon to the table.

* * *

 **In the now deserted Zora's Domain, a stray bokoblin wanders in and pokes at a viscous fluid on the floor. It is then attacked from behind by an unknown creature. It's screaming stops as a screeching sound reverberates through the halls and a dome shaped shadow with four protrusions underneath it floats away.**

 _To be continued._

 **Author's note: That can't be good. So, I finally got around to finishing this chapter. I know that it was a bit of a slow chapter, but don't worry; it'll pick up soon. And yeah; it was obvious what's going on in Zora's Domain, right? XD**

 **Once again, rate and review please!**


	6. Chapter 6 The New Terror

**Chapter 6: The new terror**

"My mommy always said there were no monsters - no real ones - but there are." –Newt (Aliens)

* * *

 **The trio, along with Sidon, head to Zora's Domain to investigate the identity of the creatures that attacked the Zora's (Purah and Symin had stayed behind in their lab to try and reestablish connections with the other towers). Soon enough, they reach the Lanayru region.**

"Alright, so which way should I take you?" Samus asks.

"Hmm, the domain is east of here. If you fly that way, we should reach it soon- WHOA!" Link is interrupted by a red stream of energy that nearly hits the ship.

"What was that?!" Zelda shouts as several more streams fly towards the ship.

"Someone, or something, is firing at us! I can't advance any further; I'm bringing the ship down!" Samus exclaims as they land at the Lanayru wetlands. The group then exits the ship.

"I guess we're walking towards the domain." Samus comments.

"But, what was shooting at us?" Zelda questions.

"I don't know, but whatever it was definitely doesn't want us getting near the domain." Link answers. "There's probably something there that needs to be defended."

"Well, there's no point in guessing; let's move on." Samus says. Before they get any farther, the hatch from the ship opens up and Sidon jumps out, covered in bandages.

"Hold on! I'm coming with you." Sidon declares. "You'll need my help to reach Zora's Domain."

"Prince Sidon, shouldn't you be resting?" Zelda asks with concern.

"I appreciate your concern, but I cannot; not while my home is in danger. Besides, there is a pack of Lynels that have claimed territory here. If we do manage to run into them, you will need all the help you can get."

"Let him come along; he helped me out with the divine beast, so this shouldn't be much different." Link says. "He'll need a weapon though. Ahh, I've got it; hold on a minute." Link runs back to the ship to retrieve something. At that moment, something begins to move through the ground before erupting from it; revealed to be a trio of corrupted lizalfos, each one hold a forked lizal spear and growling at the trio.

"Sidon, your highness, get behind me!" Samus orders as she aims at the attacking lizalfos.

"Sidon!" Link shouts to Sidon as he throws him a spear, which he catches. Not giving thought as to what it is, Sidon jumps in and engages the lizalfos, Link joins him and Samus stays back to guard Zelda. Link goes for his sword, but one of the lizalfos extends its tongue at Link and uses it to propel itself and then ram him. Sidon goes to try and help Link, but is stopped by the other two lizalfos. Thankfully, Link gets back up quickly and, with the augmented strength that the suit provides him, elbows the lizalfos into the other pair. Sidon rapidly stabs one of the lizalfos before skewering it and then tossing its carcass aside. Link dodges the attack of the second lizalfos before swiftly getting behind it and slashing downward, ending the fight. The last one tries to blind side Link, but he moves out of the way, leaving it open to a slash from Sidon, sending it falling on the ground. Link jumps over and finishes it off with a downward thrust as the lizalfos makes its dying croaks.

"I think that was all for now." Link removes the master sword, the blade shining as it's pointed upward.

"I detect no other creatures in the vicinity." Virginia (from inside Samus's suit) confirms.

"Then, we shouldn't waste any more time. Let's move before any more of those beasts appear." Zelda declares as the group starts to move forward. Sidon, on the other hand, stops to observe the 'spear' that was handed to him by Link and realizes that is not a spear at all; it is the lightscale trident, the cherished weapon belonging to Mipha, the previous Zora champion and Sidon's sister.

"Link, this is…" Sidon comments in bewilderment.

"Yes, I think it's time that I return it to its rightful owner; that would be you." Link declares.

"But, this belonged to my sister. Therefore, it is rightfully yours. She would want it that way, because she lov-"

"I know. I'm well aware of it." Link calmly interrupts. "But, I don't need it to remember her. Seeing her spirit at peace after freeing Vah Ruta is more than enough to keep her in my memory."

Sidon looks intently at the trident before finally speaking up. "...I understand Link, bear in mind though, that if you want this back, you need only ask."

Link nods in response and the group makes their way through the wetlands. On another note, Samus realizes what was inside the large bag that Link had placed inside the ship; it held the champions weapons all along, so Samus concluded that Link wants to return them as a way of remembering their beloved champions of each respective race.

* * *

 **The Inogo Bridge**

"Hey Sidon, this is where we first met." Link says with a nostalgic tone.

"Yes, I first met you here when I needed help to appease Vah Ruta. Two months ago still feels like yesterday." Sidon responds. "Who would have thought that we'd be in another situation again?"

"Well, it's not like Link to abandon a friend in need." Zelda cuts in.

"Hold on a minute, don't you guys hear anything?" Samus speaks up and the group nods dismissively. "That's right; I don't hear anything at all. Not a single beast is around here, I thought there would be packs roaming the area."

"Something's not right." Link cautiously comments. "I think we should keep moving."

"Wait, look there." Zelda points at a footprint on the mud after they pass the bridge. "That's a Lynel, isn't it?"

"Yes, we must be close to them." Sidon answers as he wields the trident. "Stay sharp, they could show up at any moment."

The group divides into two pairs (Link and Sidon/Samus and Zelda) and quietly walk up the hills. Sidon points out that he can see the back of a Lynels head, so Link pulls out his ancient bow and prepares to fire an arrow. Sidon gives the go ahead as he jumps up with the trident pointed downward. Link shoots the arrow at the back of the Lynels head, but is shocked that the Lynel disintegrated completely. Sidon lands on the ground it was on, taken by surprise that the Lynel turned to dust. After a few seconds, he points out that the other five Lynels have been "petrified", each in a different stance.

"What did this?" Link says with deep concern.

"It must have been the creatures. Look, they were firing at all sides." Sidon points to the shock arrows lodged on the ground, trees and rocks.

"By the looks of it, there were no more than eight of them. How'd they miss every single one of them?"

"They were probably the smaller ones; those tend to fly around alot."

Just then, some unseen creature flies overhead, earning alarm from the two.

On another area, Samus is left stunned at the sight of a moblin hunched over and completely dried out. She scans the body and confirms the cause of death: metroid predation.

"No...Link! Sidon! Where are you?!" Samus shouts in panic. "Regroup right away!"

Alerted by Samus, the duo runs over to where she is. "What's the matter? You sound like you've seen a ghost." Link comments.

"Sidon, those 'flying jellyfish', did they look like this?" Samus projects a metroid hologram from her helmet.

"Yes, exactly that! Do you know what they are?" Sidon responds.

"Yes, they are metroids; energy parasites that feed on an organisms life force, leaving only a brittle husk." Samus confirms as she readies her ice beam. "Link, do you have any ice arrows?"

"Plenty of them. Why?" Link answers.

"You'll need them on the way to the domain, come on." Before they move, Link notices that Zelda isn't present. The three then begin calling out to her, with quickly growing concern.

* * *

"Hmm, the subject appears to have been turned into a dry shell of what it used to be." Zelda writes down in her journal, which she decided to bring along, about the bokoblin corpse she stumbled across. She reaches out to touch it, only for it to crumble into dust. "And has lost all semblance of structural integrity, *cough*." Zelda gets up, pats herself of any dust, and prepares to take photos of the other corpses. After taking one, a small metroid floats in front of her viewfinder, all the while chirping.

"What is this? A new species?" Zelda lowers her slate to inspect the metroid. "This must be the creature that Sidon was talking about. But, it looks harmless- ahh!" The metroid dive bombs Zelda with its fangs opened wide, which she manages to dodge. The metroid starts circling Zelda, confusing her, then ramming on her back and knocking her down. It then tries to latch on to her, only for Zelda to grab it as it furiously tries to sink its fangs on her head.

"Help! Somebody!" Zelda desperately shouts as her arms start to give way, causing her to question why such a small creature would be so strong. As its fangs are mere inches away, Link appears and kicks the metroid into a bush. He then kneels down to see if she's injured while Sidon stands watch.

"Are you alright?"

"I think so." Zelda replies, the fear present in her voice.

"Princess, how could you wander off like that? This place is no longer safe for us. No offense, Sidon."

"None taken." Sidon replies before holding his trident forward. "Here it comes!"

The metroid flies towards the trio, but is instantaneously frozen and then crushed by Samus.

"Now you see why should have ice arrows ready? They can't take the cold." Samus comments while helping Zelda to get back on her feet.

"What was that thing" Zelda questions.

"A metroid, like the ones I told you about. The very same from SR388."

"But, you said that you destroyed them all." Link retorts.

"I know, which is why this is odd. First the elite pirate and now a metroid. This is all connected somehow."

Suddenly, slow clapping is heard and Silas steps out from behind a tree.

"Very good, I hoped you were more brains than brawn and you did not disappoint." Silas mockingly applauds the group.

"Silas, so you are still alive." Link comments while moving Zelda behind him, before looking at Silas phazon powered right arm. "I see you grew your arm back."

"Yes, I've thought about that moment since that night in the rain." Silas brings up his arm before smiling maliciously. "But, life goes on. I now have a new calling."

"Enough of this, what do you want?" Sidon demands as he points his trident at Silas.

"The subjugation of the world, that's all."

"You know that you will not have your way; we will stop you." Samus sternly retorts.

"This won't end well for you, remove this barrier and surrender." Zelda demands.

"Heheh, you think I set up this barrier? That was the work of our new god. She spreads this purity to right our wrongs."

"New god? What are you talking about?" Link questions.

"You'll see; everyone will. For now, have fun with her creations. I'm sure you'll find that their appetite is plentiful to say the least. Enjoy your little expedition…while you can." Silas then disappears in a flash of red light.

"So, Silas isn't the one behind this. He's just an underling." Zelda concludes.

"That means we've got a new challenger in the kingdom." Sidon comments.

"Regardless, we're going to stop this perpetrator and their machinations." Link declares while sheathing the master sword. "We should get moving."

"Agreed, but remember; if what Silas says is true, then there are several more metroids in the region. So everybody; don't stray." Samus says to the group before they walk off.

* * *

After 13 uneventful minutes, the group hears a woman screaming and rushes to her location. They arrive and witness a small group of Zora's being attacked by several metroids. The guards try to fight them off, but all except two of the five are leeched of their energy by the metroids, after which two of the metroids fall to the ground. The rest of the metroids lunge at the survivors, but Link shoots ice arrows at them and they fall to the ground, giving Sidon the opportunity to shatter them.

"My prince!" One of the surviving guards speaks up. "Praise Hylia that you're safe. But what are you doing here?"

"I've brought help; Link has once again come to our aid." Sidon declares as Link lowers his bow.

"I've brought some friends of my own." Link gestures to both Zelda and Samus, causing the Zora's to bow at Zelda's presence. Before they can question them, Sidon confirms that Samus is an ally. The guards explain to Sidon that they've been scouting the area to search for any stragglers that got left behind, running into several metroids and keeping them at bay (relatively). But, they were attacked front and back before the group reached them.

"Goodness, you've been through quite the ordeal." Zelda comments. "Have you run into any other beasts apart from them?"

"No, your highness. Just these 'metroids' and-"

"THAT!" One of the Zora children shouts as the two metroids that fell to the ground rise up and begin to crack. In a matter of seconds, a creature with two red compound eyes, three large fangs surrounding a leech-like mouth outlined with smaller teeth, four budding limbs, a plated exoskeleton growing along the dorsal region and a transparent membrane with a nucleus on its underbelly emerge from the two metroids.

"There! Those are the insects I told you about!" Sidon shouts.

"Category one: Alpha Metroids." Virginia confirms after scanning them.

"Everybody, stand back!" Link shouts while aiming at the alpha metroids. Link fires an ice arrow at one of them, but the arrow only manages to scratch its carapace. Enraged, the alpha metroid screeches as it lunges forward, radiating energy all over its body. Link dodges this and the metroid hits the rocks behind him, crushing them.

Link, you need to hit their nucleus!" Samus shouts as she fights the other alpha metroid, earning a 'what?!' from Link. "Damn it...the underbelly! Shoot its underbelly!"

"Got it!" The alpha metroid lunges at Link again, but he slides under it and lands an ice arrow at its nucleus, causing it to screech in pain and inhibiting its energy charging abilities. The alpha metroid recomposes itself and sinks its fangs on Links arm but thanks to the added strength of the suit, he pries the metroid from his arm and then runs the master sword down its mouth. The remaining metroid circles Samus, but then makes a beeline for the surviving group, ignoring the terrified Zora's altogether and rushing, surprisingly, for Zelda.

"Your highness, get out of the way!" Samus shouts as she tries to fire at the metroid to grab its attention. Zelda responds by ducking down, the metroid just barely missing her. It tries to double back to grab her, but Sidon swats it away with his trident.

"Why is it after her?" Samus questions while running towards Zelda. Link uses Revali's Gale to launch himself into the air and, using his finely tuned reflexes offered by his suit, shoots an ice arrow into the alpha metroids mouth, freezing it instantly and allowing Samus to shatter it with a missile.

"I think that's all of them, for now." Sidon comments.

"Is everyone okay?" Link asks to the survivors and they all confirm him.

"Listen, I know that you three need to get to the domain, but I ask you to help my people get to the safe zone where my father and the rest of us are hiding. We may not make it there without you." Sidon pleads with the trio. After a few seconds of pondering, Zelda speaks up.

"We can't abandon them; I say we should deviate from the task for now and escort these people to safety." Zelda says as both Link and Samus agree. Sidon thanks them and they make their way to the safe zone; with Link and Sidon at the head of the group, Zelda in the center with the others and Samus covering the rear. Unbeknownst to them, a creature with three eyes on both sides of its head watches them walk away.

* * *

 **The entrance to the safe zone**

"Alright you three, the safe zone is through this water tunnel." Sidon explains. "Do you have some way of making it without difficulty?"

Link activates his helmet, which allows him to extract oxygen from the water. Zelda activates a helmet reminiscent of Samus's own, with a blue visor instead of green, offered by her for these sorts of situations. Finally, Samus activates her gravity suit, a purple variant with blue designs of her varia suit.

"Ready." The three speak in unison.

"Oh...Very well then. Alright everyone, we're moving in the same way we escorted the survivors. The tunnel is 30 meters long; we will not stop moving until we reach the other side. Now, Link and your highness, you move behind me, the survivors will follow behind you and Samus will cover them." Sidon explains before gracefully diving into the tunnel.

"Stay close to me, alright?" Link says as he grabs Zelda's hand.

"Y-yes." Zelda confirms as she blushes. The two then dive in together, followed by the survivors and Samus. They steadily swim through the tunnel, which is lit thanks to luminous ore deposits that line the walls, all the while Samus and the guards cautiously watch the front and back of the group. Roughly 18 meters in, one of the guards shouts in panic as he points to several metroids and alpha metroids following behind them.

"Sidon, they followed us!" Samus alerts everyone while firing missiles at the incoming metroids. Sidon orders everyone to swim faster as Link doubles back to offer assistance, only for Samus to hold her hand up. "Link, take the princess and go ahead!"

"We can't leave you behind! Let us help you!" Zelda shouts in worry.

"Just go, I'll be fine! Get these people to safety!" Samus orders as she's surrounded by the metroids. "GO!"

Link hesitates briefly before swimming towards the survivors and coercing them to keep swimming, all the while telling Sidon to grab Zelda and to get her to the other side.

"Prince Sidon, let me go! She needs our help!" Zelda protests as Sidon takes her to the other side of the tunnel.

"I can't do that, your highness; I need to get you and my people to safety." Sidon denies her request.

"And what about her?! Is she not a priority?!"

"Princess, if we stay here, those beasts will kill us all. She's giving us the time we need to escape, we have to take it!"

"But…" Just then, Link swims up to them.

"Your highness, I want to help as well, but we need to get these people to safety. She says that she can do it, so just trust her." Link explains in a comforting tone, which Zelda responds with an insecure nod. The trio manages to get the survivors to the other end of the tunnel, which Samus notices.

"They made it to the other side, Samus." Virginia confirms.

"Good, that means I can use this." Samus ducks down as the metroids overwhelm her. From beneath them, a bright light emanates.

* * *

After getting the survivors to safety, Link runs back to the tunnel.

"Everyone stay here, I'm going back down to help her."

"Please hurry, Link. There are a lot of them." Zelda comments as she removes her helmet. Just as Link prepares to dive, an explosion rocks the area and water from the tunnel blasts Link away from it. Link gets back up and, with a sense of dread, he runs towards the tunnel.

"Samus!"

"Where are you?!" Zelda joins to shout for Samus to answer

"Samus, answer us!" Link shouts in despair.

No response. Link finally falls to his knees and lowers his head.

"Samus…" Zelda covers her face and silently cries. From behind Sidon lowers his head in remorse while the confused crowd looks on. Just then, a purple ball erupts from the tunnel and lands behind the pair, much to their surprise. The ball then unfurls and Samus emerges from it, who falls on her back and then deactivates the suit.

"Ugh, remind me to never do that again." Samus wearily comments, to which Virginia replies that she'll do it anyway.

"Samus!" Zelda runs over and joyfully hugs her, causing Samus to exclaim in slight discomfort from her bruises. "You scared us!"

"I just needed you out of the tunnel, so that I could detonate a power bomb. It destroyed them all."

"That was one hell of an explosion. You shook the cave." Link comments as he places a hand on Samus's shoulder. "But I'm glad you're ok." Samus smiles at Link words, and then places her hand over his.

"Ha-ha! I just knew you couldn't fall that easily, I believe in you!" Sidon gives a sharp toothed grin and flexes his right arm. The trio also smile and laugh, grateful that they made it.

* * *

After recovering enough, the survivors walk further inside the cave and locate the rest of the Zora's hiding place. The survivors joyfully reunite with their families and Sidon runs over to his father, King Dorephan (a large blue and white Zora with a red sash across his chest and shoulders, with a star shaped emblem in the center of it and connected by three gold chains under his right arm. Along with several intricate silver apparel on his wrists, chest and head, as well as a noticeable scar on his forehead.)

"Sidon, praise Hylia that you are safe!"

"Father, I'm glad to see you are all well! I've brought more help." Sidon points to Link and Zelda, who approach them.

"Link! Good to see you again and unharmed." Dorephan smiles before noticing Zelda. "Princess, what an honor to have you here! But, why are you here at this time? Our domain is no longer safe."

"It is a pleasure to see you again, King Dorephan. But we are here to stop this blight over the land. We know what it is. Samus, please come over here and explain what is going on." Zelda gestures to Samus to come closer. She then explains what the phazon is and where it is coming from.

"So this 'phazon' is not from this world after all?" Muzu, the advisor of the Zora royal family, speaks up. "And what about these creatures that infest our home?"

"We believe that they're coming from the phazon, we just don't know how." Link offers an explanation.

"We just need to know where the barrier originated from, then we can figure out a way to disable it." Zelda comments.

"I think I know where it came from; those creatures came from behind Zora's Domain and the barrier followed them, covering the sky in blue." King Dorephan explains.

"Father, you can't mean-" Sidon comments before being cut off by the king.

"Yes, my son; I believe the barrier came from the same place as Divine Beast Vah Ruta."

Link and Zelda stare wide eyed at this possible revelation. Sidon, however, reacts angrily.

"Wretched creatures! Will my sister never be allowed to rest in peace?!"

"Calm down Sidon, we now have a place where we can start from; we need to head towards Vah Ruta. If it started there, Samus can purge the phazon from it." Link explains.

"Yes, our destination should be this 'Vah Ruta' and see what the damage is in its area." Samus adds.

"If you plan on going there, to Vah Ruta, I implore you to be careful; those monsters might be the most concentrated there, don't let your guard down." King Dorephan warns the group.

"We will your majesty. I've dealt with them before; these two will be safe under my watch" Samus declares. Just then Virginia alerts them.

"Samus, a metroid is approaching our location, and it is a category two." Virginia states.

"Link, there's a metroid on its way here. Stay put, I'll handle it."

"No, you stay here; I'll face it." Link declares while brandishing his sword and shield. "Just keep the others safe."

"Link, be careful. This creature is stronger than the others, I can feel it." Zelda warns about the incoming metroid.

"It's a category two; a Gamma Metroid." Samus adds. "Remember what I told you about the alphas; just take note that these are much bigger and stronger than them."

"I'll handle it." Link raises his sword skyward and makes a declaration. "I am Link, champion of Hyrule and loyal protector of Princess Zelda. We will not falter in the shadow of this new threat; we will rise again and wipe out this plague, just as we did for the Calamity. We will prevail!"

The Zora's begin cheering as Link faces the tunnel and awaits the metroid. Sure enough, a large alpha metroid-like (double its size) creature emerges, with a pair of three red eyes, fully formed insect like legs and three enlarged fangs surrounding its leech like mouth. The gamma metroid stares at Link and then screeches at him. Just then, it stares at the Zora's (who in its vision appear as surrounded by white auras) and then stares at Zelda (who appears as surrounded by a gold aura). The metroid appears to drool and flies towards Zelda, knocking the others away. Link manages to grab it by its small tail and throws it back to the entrance. Enraged, the gamma metroid decides to face Link, hissing its anger at him. The Zoras start hollering and pumping their arms in the air, cheering for Link to be victorious (Zelda looks on in worry and Samus never taking her eyes off the metroid). The metroid charges at Link, who jumps out of the way and slashes at its carapace. It turns around and fires a brief stream of energy which Link blocks. It then flies towards him in an attempt to bite down on Link, who slides under it and jabs an ice arrow in its nucleus, causing it to fall to the ground. Further enraged, the metroid forces Link to the ground and once again tries to bite him. Link holds the master sword horizontally to keep it from biting him and manages to kick it off. The master sword still in its mouth, the metroid throws it aside and charges at Link, the ice removed from its nucleus, who bashes it across the head with his shield. While it is disoriented, Link runs for the master sword and retrieves it. Just as he turns around, the metroid tackles him into the water tunnel. The Zora's stare in complete silence, waiting for one to emerge from the tunnel (Zelda in particular anxious for Link to emerge). The Zora's begin panicking as the gamma metroids carapace emerges from the tunnel, only for it to fall limp on the ground with the sword protruding from its nucleus and Link climbing up from the tunnel to the cheers from the Zora's and Zelda running to embrace him, all the while smiling, and Samus walks up to pat him on the shoulder.

"You were right about him, my prince; he's our best hope to survive this." Muzu confirms with a smile.

"Yes, I expected no less from the man my sister declared her love for." Sidon comments. "Now, it's up to him and his new ally to purge this infestation and restore all of Hyrule to its glory."

"My son, they will need you as well. Do not forget that you are just as important to Link and the princess." King Dorephan states. "Make your sister proud."

Sidon smiles at his fathers words as the Zora's applaud and chant Links name. He then looks at the lightscale trident and grips it tightly, finally accepting his sisters legacy and resolving to protect his kingdom.

 _To be continued_

* * *

 **Authors note: Yeesh, this took me quite a while to get up off the ground, but I did it, Hahah. In case the metroid fans were wondering, yes; the alpha and gamma metroids described in the chapter were the same designs from Metroid: Samus Returns. Those metroids were actually much more intimidating than the ones from the original Gameboy version and I just had to include them here. Stay tuned for the next chapter and once again, rate and review please! :)**


	7. Chapter 7 Isolation

**Chapter 7: Isolation**

"Danger is real, fear is a choice."

The quiet lands of Lanayru are disrupted by the sounds of a young woman running from an unknown attacker. After reaching a recently built house, she closes the door, locks it and places a table in front of it. She then goes deeper inside the house and finds a sword, which she picks up and then jumps as the sound of the door being forced open alerts her. She looks back and sees the door torn off its hinges and the table split in half. Fearful, she slowly walks to the back of the room, never taking her eyes off the entrance, but stops after hearing a thud from behind her. The young woman turns around and the attacker towers over her (growling all the while), its hideous visage reflected in her widened emerald green eyes. The attacker then roars at her.

* * *

 **6 hours earlier**

"Like this?" Zelda asks while standing upright with her arms spread out.

"Yes. Just stay still, I'm going to scan you. The fact that several metroids skipped over us to get to you was no mere coincidence; they wanted something from you." Samus explains. "Something that we can't see."

Samus scans Zelda, the latter being mesmerized by the almost water like surface of the scan visors light reflected on her.

"Bioscan complete." Virginia gives the report. "Subject is a young female Hylian. Bioscan's indicate healthy life signs and the presence of an unknown energy source. Energy is reminiscent of subjects life force, but on a much grander scale."

"There's another energy source within you, princess?" Samus questions.

"Well, there is a power that is passed down within my family; it's a sealing power that was strong enough to stop the Calamity. Why do you ask?"

"I think that's what the metroids are after."

"Hold on. What exactly are you talking about?" Link interrupts.

"I think that her sealing power is tied to her life force. It is probably stronger than any other living creature here. Bearing that in mind, the metroids see her and go into a frenzy; intending to feed on her life force as if they were being beckoned by it."

Zelda reels back in fear over Samus's explanation. After some deliberation, the decision is made to leave Zelda in the care of the Zora's and for Link and Samus to continue to Vah Ruta without her. Zelda, however, was angered by this decision.

"I refuse to be left here while you continue on!"

"Princess, this is for your own good. You stay here and you'll be safe." Link explains.

"I'm the one they want; I stay here and they'll come for us eventually! How many of these people have to die before they get to me?!"

"Princess-"

"I have a name! It's Zelda; not 'princess', not 'your highness', Zelda! Their lives are just as important as mine; I will not let them die because I was the one the enemy is after. Besides, you said that you are my protector; is leaving me out of your sight protecting me in any way?"

Link, taking all of her words into account, comes to a surprising conclusion; she was right. Leaving her here as a "beacon" of sorts to indirectly lure the metroids to the safe zone would result in the deaths of all the survivors. Also, that he would protect Zelda from anyone and anything, he was nowhere near willing to repeat his mistakes from a century ago.

"You must promise to stay in my sight at all times, in Samus's sight as well. Don't move unless I say. Don't make a sound unless I say. Do you promise me?" Link lays down the rules.

"Of course, I leave it all in your hands." Zelda answers.

"Then let's not waste any more time. We're moving out." Link says before being stopped by Samus.

"Link, are you sure that this is a good idea? She's basically a walking beacon to the metroids."

"We won't be with anyone else; if push comes to shove then we'll handle it."

Samus, not fully convinced, decides to listen to Link and walks over to Zelda.

"Princess- I mean Zelda, let me see your journal for a moment." Samus asks and Zelda hands over her journal, which she then imprints paragraphs and images of the metroid species. "Here, with this you'll be able know what types of metroids we may come across."

"Wow, you've seen all of these?" Zelda asks and Samus nods. "Category one, category two, category three? What's that one like?"

"There will be plenty of time to read up on them later. Right now, we need to head out." Link speaks up as he walks to the safe zone entrance.

"Link, your highness and our new friend; I thank you for your help. Now, you plan to head to their territory?" Sidon asks.

"Yes, if we can stop it at the source then that should be our next destination." Zelda declares. "Besides, Samus will help us every step of the way. Won't you?"

"I'm not going to stop now." Samus smiles and pats Zelda's back, earning a smile from her as well.

"Well, if that is your plan; then I wish you luck. Those beasts are ruthless, but if anyone has a shot at beating them, it's you."

"We'll handle it. You'll have your home back, Sidon. You've got my word on it." Link promises to Sidon.

"There's no doubt about it; I believe in you!"

The trio jump into the tunnel and Sidon looks on as it is sealed with a large boulder by the Zora guards.

* * *

After leaving the tunnel, the trio makes their way to Zora's Domain. Samus noting that it is late in the afternoon and that the metroids become more active at night, so they should find shelter soon. On another note, Samus nudges Link's shoulder while gesturing to Zelda, who is reading up on her journal. Link, letting out a sigh, realizes what Samus is implying and walks up to Zelda.

" *ahem* Princ- I mean, Zelda?" Link realizes how odd it is to speak to her in such an informal way.

"Yes? What is it Link?" Zelda asks, while not taking her eyes off her journal.

Deciding that asking directly might "put her on the spot", Link talks to Zelda as if it was any regular conversation. "Well, I just wanted to know what you planned to do when this is all over. What you want to do for the future and such."

"Hmm, well first of all, the castle will need to be completely repaired. Then, the reunification of the land can officially begin. From there, we'll just take it one step at a time."

"Ah, good. But, there's nothing else that needs to be done? Nothing _very_ important that slipped your mind?"

"...Nope. Nothing at the moment."

Samus, growing weary of the "conversation", tells Link (quietly) to just mention it now. Link takes a deep breath and finally asks directly.

"Not even...the coronation ceremony?"

Zelda stops abruptly and Link feels a chill go up his spine. After a few seconds, she answers him.

"Ah yes, that. That is important, isn't it? Well, that is still a ways off, so I don't need to worry about it now."

Based on her tone, Link and Samus realize that Zelda isn't setting it aside for later; she is up front avoiding the subject altogether. But why?

"May I ask when you'll tackle the matter?"

"Another time."

"When will that be-"

"WHEN I SAY IT WILL BE!" Zelda defensively yells. "We're done talking about this, now drop it and let's go…" Zelda continues to walk in a huff. Link decides to drop the matter for now and silently walks behind her while sulking. Samus walks up beside him and reassures that they'll find another way to get her to open up. Just then, Link feels a surge in his head and runs toward Zelda and tackles her to the ground. Before she can protest, several arrows fly above them.

"It's the Yiga!" Samus shouts as she begins firing missiles at the cliffs where the arrows came from. Link then hurries Zelda to take cover in some bushes before doing a 180° turn and slashing diagonally at a Yiga footsoldier that just materialized behind him. Switching to her plasma beam, Samus blasts a hole through another Yiga before being blindsided by another footsoldier that is emanating phazon energy from his body. Samus regains her composure and Virginia reports this.

"Samus, that footsoldier has entered hypermode. Confirming the same case from Kakariko village during their botched invasion."

"Unbelievable; this 'god' of theirs gave them hypermode?" Samus then jumps over the footsoldiers phazon whip and drop kicks him in the face, incapacitating him and then calling out to Link. "Link, use the new arrows! You'll overload the empowered Yiga!"

Link nods as he pushes away a hypermode Yiga and then, using his finely tuned reflexes, shoots a glowing blue tipped arrow at the soldier, causing him to convulse and writhe on the ground before dissolving into a pool of phazon. No time to comment on the gruesome sight, another footsoldier tries to hit Link from behind. He turns back to defend himself, only for the footsoldier to fall dead at his feet, an arrow sticking out from the back of his head. Zelda, having taken a duplex bow from another dead Yiga, shot an arrow directly at the attacking footsoldiers head. Impressed by her pinpoint accuracy, Link hands Zelda two bundles of arrows and bomb arrows.

"Here; make them count!" Link says as he rejoins the fight. At the other end of fight, Samus struggles with a hypermode footsoldier, internally wishing that she still had her PED (Phazon Enhancement Device) suit as it would have done wonders against the Yiga. Eventually, an ice wizzrobe emerges from the trees, however this wizzrobe is covered with upside down Sheikah markings, indicating that it is being used by the Yiga. Link, realizing that it is behind the sudden cold temperature and clouds, shouts to Samus.

"Samus, that creature is causing the cold! Shoot it with something heated, you'll melt it instantly!"

As if picking up on this, the wizzrobe begins hurling chunks of ice from its rod, creating several stalagmites and lowering the temperature further. Soon, Link and Zelda move sluggishly as they start to succumb to the cold. Not wanting to waste any more time or leave Link and Zelda exposed to hypothermia, Samus fights off the Yiga, readies her plasma beam and fires off a charged shot of it before being hit by a surge of ice, freezing her. Fortunately, the shot connects and the wizzrobe is instantly evaporated. The sky clears and the temperature regulates itself.

"Stupid fools, you've chosen your own demise! Everyone fall back!" One of the footsoldiers shouts as the surviving Yiga escape. Samus breaks free of the ice and walks over to the pair.

"Are you two alright?"

"Hah...I'll live." Link exhales.

"I'm fine." Zelda responds.

"What happened? They just left." Samus inquires.

"Was that wizzrobe important to them or something?" Link asks before being interrupted by loud screeches from all directions. Samus checks her radar and sees several metroid signatures closing in on them, finally realizing why the Yiga ran off; they were using the ice wizzrobe to keep the metroids away!

"Both of you; huddle up! We've got metroids incoming!" Samus shouts as she readies her ice beam. She then asks Link to extend his right arm, which has a circular pattern that appears when she connects her arm cannon, causing it to glow.

"What are you doing?"

"Upgrading your suit; you can now imbue your sword with fire, electricity and even ice. Your neural interface lets you choose by thinking one of the three. Now, get ready."

A metroid flies towards them, but Zelda shoots it down with an arrow. After this, a group of larval, alpha and gamma metroids rush them. Link chooses ice for his sword, causing it to glow blueish white, and slashes at a pair of metroids; bifurcating and freezing them at once. An alpha metroid rushes from their right side and Zelda obliterates it with a bomb arrow to its mouth, while Samus destroys another pair with her super missiles. A trio of gamma metroids fly down and run towards the group; Link runs at the nearest one and runs the master sword through its mouth, freezing it from the inside out. The second one rushes at Zelda, but she fires a bomb arrow at it, which throws it at some nearby bushes. The last one is rushed and then electrocuted by Samus's wave beam, followed by Link, who stabs it on the top of its head. They turn around to kill the remaining metroids, but are shocked to see Zelda take them down with nothing but arrows, each one with startling accuracy. With the metroids taken care of, the trio catch their breaths.

"Where did you learn to shoot like that?" Samus asks, genuinely curious.

"I just trained with a bow and arrows when I was younger; it just...clicked with me." Zelda explains.

"She's actually much better than me, hahah." Link adds, a small hint of pride present in his words. "Well, if we're ready, we should continue on to the domain. There's still a few more meters between here and there-"

Just then, it happened in the blink of an eye and time seemed to slow down; Samus was shot from behind by an energy blast, knocking her down and then Link being rammed against the rock wall. Link looks up and sees the gamma metroid grappling with Zelda, having survived being shot by the bomb arrow, and trying to sink its fangs into her. To his horror, the metroid forces Zelda to the edge of the path, intending to fall down with her.

"Ahh! Link!" Zelda shouts in terror as she begins to lose her footing, holding her hand out to him and letting the metroid suck out some of her life force, screeching in what appears to be 'delight'.

"No!" Link jumps to his feet, disoriented, and desperately reaches out to her. Unfortunately, he misses by centimeters. "ZELDA!"

Zelda screams as she falls over the edge with the gamma metroid into the rapids below. Seconds later, Samus gets back up, groaning in pain.

"What was that?" She then looks over at Link, who is on his knees, by the edge. "Link, what's the matter? Where is Zelda?"

Link turns around, tears in his eyes, and answers her.

"I lost her…"

* * *

 **On the shores of Mercay Island, on a far side of the Lanayru wetlands, an unconscious Zelda washes up albeit alive. Moments later, she wakes up.**

"Where… am I?" Zelda wearily gets up, but cries out in pain as she sees one of the metroids fangs lodged in her left bicep. She grabs the fang and pulls it out, exclaiming in pain as it is removed. Tearing off her sleeve, she uses it as a makeshift bandage to stop the bleeding. Taking into account of the area, Zelda walks towards the river as it would lead back up to Link and Samus, along the way she finds the duplex bow, which had been damaged by the fall and rendering it useless. Undeterred, she walks up the hill, holding onto her arm.

* * *

Meanwhile, back up with Link and Samus.

"Virginia, tell me what I want to hear…" Samus commands, the fear and despair present in her voice.

"...The princess is mobile." Virginia reports, bringing up a blue light in the radar, indicating Zelda's position. "The tracker is functioning properly." Samus smiles at this.

 **Flashback**

"Besides, Samus will help us every step of the way. Won't you?"

"I'm not going to stop now." Samus smiles and pats Zelda's back, placing a glowing green light that becomes covered by her hair. Samus had placed a tracker on her.

 **Flashback end**

"Link, I've got her; she's headed back up to us."

"She's alive?!" Link stands in front of Samus and grabs her shoulders. "Where is she? Is she alright?"

"Calm down, I can't see how she is. But I know that she's trying to get back up here. We should go get her first before anything else, and then we need to get to some place safe for the night."

"I agree. So, what are we waiting for?" Link readies his sword and starts to follow Samus down the path. Just then, Virginia begins alerting the pair.

"The princess is deviating from the path and she's moving erratically. I believe that she is being chased by something."

Fearing the worst, they run as fast as they can to her position.

* * *

Going up the river, she finds her bag hanging on the side of it and reaches out to grab it. Just then, the gamma metroid falls on top of her, causing her to scream. She pushes it off and is surprised to see it completely unresponsive. After poking it with a branch several times, she concludes that it died in the fall. Relieved, she picks up her bag and continues forward. Unknown to her, the gamma metroid yellows and then crumbles away, revealed to only be an empty shell.

Deciding that she needs to stop for a moment, Zelda reaches into her bag and pulls out her journal. Skimming through the entries that Samus gave her, she stops at a particular one and reads aloud.

"Category three: Zeta Metroid. The second to last stage in an ordinary metroids lifecycle, this creature is by far the most dangerous metroid. No longer able to fly, it can climb on walls, ceilings and most other surfaces with its sharp talons. The most distinguishing aspect of a zeta is its tenacity; it has a habit of choosing a prey and then relentlessly hunting it until it is finally captured. Any other person who has been pursued by a zeta metroid is usually never found. Side note; the gamma metamorphs into a zeta after a long period of time, feeding on life energy in an attempt to rush the transformation."

As she finishes reading, a viscous fluid falls on her head and she looks up to where it came from. She stares wide eyed as a large creature with an elongated head, leech like mouth, 4 pairs of red compound eyes (four eyes on both sides of its head), long arms and legs ending in sharp talons, a greenish hide and a long tail emerges from its hiding spot on the moss covered canyon wall and stares back at her. There is no mistake; she is staring up at a zeta metroid. It then roars at Zelda, exposing its sharp teeth and menacingly crawls towards her. Zelda responds by slowly backing up, only being stopped by a boulder. Taking note of this, she patiently waits; sure enough, the metroid lunges at her from the wall and she moves to the side, having it crash into the boulder behind her and disorienting it, allowing her time to run back down towards the wetlands. Angered, the metroid begins chasing her and Zelda runs through a herd of water buffalo, startling and making them run at the sight of the rampaging metroid. The metroid catches up to the herd and, while trying to reach Zelda, is constantly rammed and shoved by the herd. In its frustration, the metroid begins slaughtering the buffalos, clawing, biting and shooting energy from its mouth at them. Finally rid of them, the metroid looks around for Zelda, but to no avail, until it spots a house; the door shutting as it gets into view.

* * *

Back at the hill, Link and Samus continue running towards the tracker signal.

"Link, she's in the wetlands!" Samus confirms.

"Hurry, it's not that far away!" Link says while picking up speed.

"Virginia, can you see her from the ship?"

"Negative." Virginia confirms. "She's in an area that is out of range. But, there is something else; I detect the presence of a zeta metroid in the vicinity. Also, it seems to be stronger than normal and, if I'm not mistaken, it is close to molting. Even though it has already molted from a gamma metroid."

"What?! How is that possible?!"

Before anymore can be said, they are stopped by another group of Yiga and Link angrily points the master sword at them. They then charge at the pair.

* * *

Zelda had managed to escape into a house that was recently built by the Hylian soldiers as a means to watch over the Zoras as they reclaim their lands from the monsters infesting it. In other words, a perfect place to find weapons. After barricading the door, she walks deeper inside and finds a royal guards broadsword and as she picks it up, the door forces itself open, causing her to jump and turn around and sees it torn off its hinges and the table that was in front of it split in half. Fearful, she slowly walks to the back of the room, never taking her eyes off the entrance, but stops after hearing a thud from behind her. She turns around and sees the zeta metroid standing on its hind legs behind her. As it reaches out to grab her, she slashes at its chest and then tries running outside, but grabs her and then throws her back towards the kitchen, dropping the broadsword in the process. Before she can react, the metroid grabs and forces her to the wall, opening its mouth wide with the intent to bite down on her head. Using her left leg, Zelda keeps the metroid at a relative distance, giving her just enough time to grab a nearby knife and stab it on its shoulder, causing it to roar and then drop her. Zelda follows up by grabbing the broadsword and then tries to stab its nucleus, but she misses and stabs its right arm onto the wall and the metroid roars in pain. She makes a beeline for the stairs, but the metroid grabs her by the leg, causing her to fall and it swings her side to side and destroying the tracker on her back when she hits the wall. Zelda manages to pry herself from its grip and shakily runs up the stairs, dodging the green bolts of energy from the enraged metroid. She makes it to the second floor and blockades the door with a large cabinet and then ducks down behind another cabinet and begins to shake.

* * *

Samus stands in shock as she looks at the four Yiga footsoldiers that had been slaughtered by Link, given the fact that she barely fired off a shot at all.

"We've wasted too much time, let's go." Link sternly says as he tosses away a bloodstained demon carver (a circular blade with uneven serrated edges) and continues to the edge of the wetlands, until Samus stops him."

"Link, I can't detect the tracker. I don't understand; I can't find her!"

With panic welling up within him, Link tries to figure out their next plan. "...She came down the river, right? Then we should try checking out Mercay Island first, come on!" They make their way to the end of the river, unaware of Zelda's actual position.

* * *

The zeta metroid breaks the broadsword from its arm and then runs up the stairs, but stops as it sees four doors. Like a lion stalking its prey, the metroid starts searching each room slowly. In one of the rooms, Zelda cowers in fear at the idea that the metroid is loose.

"Link... Samus… Help me… Please…" Zelda shakes with tears running down her eyes. "I can't do this alone… I'm terrified… That monster is out there, what am I going to do?" As she's pleading, Zelda hears the metroid crawling along the floor outside, forcing another door open. Finally, she whispers; "...Urbosa… I need you…"

"Don't be afraid."

"Huh? Who said that?" Zelda looks up and tries to find the source of the voice, but nothing.

"You're stronger than you think; you just need to see that."

"Wait a minute, is that…" Before Zelda can finish, the metroid tries to open the door and, after seeing that it can't, begins ramming and clawing at it. Zelda stares in wide eyed terror, before the voice speaks to her again.

"You've faced Calamity Ganon on your own; you can face the abomination in this house."

Zelda listens as the ramming causes a tarp on the cabinet to fall off, revealing several swords. She grabs a knight's broadsword and hides behind the cabinet. The metroid moves the other cabinet blocking the door enough to allow its arm through. Zelda, instead of worrying about the metroid, continues to listen to the voice.

"Only you can save yourself this time, that monster is in your element; if anyone should be afraid, it's him." Zelda's worried face begins to slowly relax. "This is your moment to prove that you can survive, to show that you are capable of facing any threat." Zelda begins to show determination. The metroid finally gets its head through the door and roars. "This is your land; prove yourself as its queen!" Zelda finally shows seriousness as the metroid slides through the door and begins to stalk inside the room. Zelda waits until it searches the other side and then she slowly walks out with the broadsword in a battle stance.

"Now!"

Zelda slashes horizontally at the metroids right hind leg, causing a large gash, and the metroids screeches in pain as it turns around and spots Zelda and then fires a green bolt of energy at her. She dodges it, grabs a spear from the ground and rams it into the metroids chest, pinning it to the wall. The metroid fires more bolts of energy at Zelda, which she evades with some difficulty before throwing a shield at its mouth, breaking some of its teeth. To her surprise, she finds a pair of ancient short swords as the metroid escapes the spear and lunges at her. She ducks down, the metroid passing over her and giving Zelda enough time to jump on its back and drive both swords into it. The metroid roars in agony as Zelda twists the blades inside of it and through reflex, it shoots a beam of red energy out the window.

* * *

Link and Samus, after reaching Mercay Island, see the red beam of energy that shot out of the house. The two look at each other and then run towards the house.

* * *

Zelda continues to grapple on the metroids back as it hits the walls in a desperate attempt to get her off. Zelda pulls off one of the swords and then stabs it into another area on its back. The metroids stands on its hind legs, gives an agonized screech and then falls on its back (Zelda having gotten off of it already).

"HAAAHHH!" Zelda drives both of the ancient short swords into its nucleus. The metroid roars exceedingly loud, before croaking weakly as it finally dies. Zelda gets up off of it and exhales heavily.

"You've done well, Zelda." The voice speaks with pride.

The door begins being forced open as Zelda looks on with exhaustion. To her surprise, Link had forced his way in and then stares at Zelda.

"Link…?"

Instead of responding, he stares at her bandaged left arm, bloodied clothes and face and slashes on her legs, as well as the dead zeta metroid on the floor. Then he runs over and hugs her firmly, causing Zelda to go wide eyed.

"Thank the goddess we found you. I thought I lost you. I'm so sorry I put you through this."

"Link, you came back for me?" Zelda asks, her voice shaking.

"Of course. I will always be here for you, even if you don't want me around. Remember?"

Samus walks in and takes in the scene, noticing the zeta metroid as well.

"Samus?"

"Hello Zelda, I'm so glad that we found you." Samus comments before noticing her injuries. Good heavens, you're hurt!" Samus responds with genuine worry.

"You two…. Thank you… for coming back." Zelda smiles as she loses consciousness, with only Link to support her.

"Zelda!"

"She is fine. The princess has simply given in to exhaustion. She needs rest now." Virginia reports as she scans her. Link sets her down before picking her up.

"Samus, you said that it's almost night. Can we make it to your ship?"

"Yes, it's less than half a mile away. We can get there in 10 minutes."

"Let's get her out of here then. We should take a look at her wounds." Link then leaves the room with Zelda in his arms. Samus takes one more look at the metroids corpse and wonders; 'did she really kill it by herself?' The group makes it outside and start towards Samus's ship. The voice speaks once more, this time with gentleness.

"Remember; I will always be watching over you, my little bird."

 _To be continued._

* * *

 **Author's note: I'm not gonna lie; I got a little teary eyed at the final sentence. If you've played the Champion's Ballad DLC for BotW, then you'll know why, heheh. Anyway, the whole point of this chapter was to establish the fact that Zelda has some apprehensions for succeeding the throne and the fact that the metroids want her life energy for reasons that I'll explain in the next chapter (unless you already found out why. :P). Also, the reason for the title "Isolation" had a double meaning; 1. The fact that Zelda was alone with no means of protection and being chased by a monstrous creature and 2. Her feeling of despair that no one is coming to help her; until she realizes that she can defend herself.**

 **Anyway, you know the drill; rate and review please, and happy new year guys! :)**


	8. Chapter 8 The Nest

**Chapter 8: The Nest.**

"There is more power in unity than division." -Emanuel Cleaver

 **After Zelda's harrowing experience with the zeta metroid, Samus and Link take her to the nearby ship for the night, as the metroids become more active now. Also, Zelda was in no condition to carry on today; her injuries needed to be looked at. After entering the ship, Samus asks Link to pass her the still unconscious Zelda, deactivating her suit as well, and sets her on a retractable table that functions as a medical zone.**

"Virginia, give me a report on her condition."

"Scanning...multiple injuries detected, moderately deep wound on left arm, no broken bones."

"Copied. Let's patch her up."

Samus gestures for Link to go sit in the pilot seat to give her some space. Afterwards, she removes Zelda's tattered clothes and injects her with an anesthetic to keep her unconscious. After bandaging the smaller wounds, Samus moves on to her left arm, which thankfully healed partially in a way that required moderate suturing, thanks to Zelda using her sleeve as a makeshift tourniquet to keep the wound as closed as possible. Lastly, Samus injects her with antibiotics to prevent any possible infections. After clothing Zelda with a white robe and then covering her with a blanket, Samus walks off to speak to Link.

"Well, the good news is that her injuries weren't too severe. She's sleeping now, so her wounds should heal quickly." Samus explains to Link, who has removed his suit and is sitting with the master sword leaning on his shoulder and hanging his head down, ignoring all of Samus's remarks. "Link, did you hear me?"

"I never should have brought her here…" Link says in a repentant tone.

Samus sighs before speaking. "It's not your fault Link; she wanted to come with us. Even though it looked bad, she held her own against a Zeta Metroid, not something many others could do." She then puts her palm under his chin so that they're eye to eye. "Alright? She did a great job and now she's safe."

"You don't understand; I'm her appointed knight. It is my duty to make sure that no harm befalls her. By bringing her here, I completely disregarded her safety." Link grips the master sword tightly in frustration. "Is that someone you'd want to trust with your own life?"

"Look, this could have happened to anyone; me, you or her. Just by bad luck, it happened to her. Once again; this was no one's fault." Samus retorts, earning a scowl from Link.

"Is that all you can say? Don't you even care?! She's lying on the table, riddled with injuries. Creatures that defy reality now infest the land in droves. Our world is only just recovering from ruin and now it's on the brink of collapse once again! And all you can say is that 'no one is at fault'?!"

Samus, keeping her calm demeanor, looks directly into Link's eyes before speaking. "Things won't always go the way you want them to; I've got plenty of experience to back up that claim." Samus speaks with a serious tone. "You're her personal guard, I get it. But, beating yourself up because you had a momentary lapse in your duty won't help you at all."

Link, hearing all her words, breaks eye contact and looks to the side. "...Then, what should I do?"

"Don't let her down again. That's all." Samus then puts her hand on his left shoulder. "And keep moving forward. Don't forget about the kingdom, Calamity, the champions, the people you've lost or K2-L. They are the force that should keep you moving forward to a better future."

Link, still with a somewhat somber expression, nods in acknowledgment. Samus gives him a soft smile before reactivating her suit. "Now, wait here; there's something I need to check in the house. I'll be back in a moment."

"Alright, I'll make sure nothing gets in." Link answers with conviction and as Samus begins to open the bottom hatch, Link stops her. "Hold on, what's K2-L?"

Samus's eyes widen with shock. "Where did you hear that…?"

"Samus, you _just_ mentioned it."

Realizing that she brought it up unwittingly, Samus gives an answer. "Oh right, it was...just one of my missions that went bad. I took it a little personally, but I moved on." Samus opens the hatch and quickly walks out. Link, not fully convinced by her answer, goes to the ships console.

"How may I be of service?" Virginia asks.

"Do you know about something called K2-L?"

"I am sorry Link, but I am not authorized to answer your question."

"Hmm, may I see Samus's other mission records?"

"Of course." Virginia shows on the screen several labels with different dates. "Touch the screen to check whichever one you want."

Link nods and then pretends to scroll through the entries. He actually had no real interest in the others, but the fact that he was allowed to see the other missions with the exception of "K2-L" means that Samus was definitely hiding something. After 4 minutes of meaningless scrolling, he decides to stop and sits down next to the sleeping Zelda. He places his hand on her cheek and, to his surprise; she leans on it and smiles slightly. Link then closes his eyes and exhales deeply.

"I won't let it happen again…"

* * *

 **Back at the house where they found Zelda, Samus reaches the second floor and begins an analysis of the zeta metroids corpse.**

"What are we looking at, Virginia?"

"Subject is a deceased zeta metroid, supercharged with an abnormally potent energy. Origin of this energy confirmed to be Princess Zelda." Virginia confirms

"I see. And what would this energy do to the metroid?"

"This energy would have allowed it to mature into a category 4 metroid within a matter of minutes instead of days."

Samus's eyes widen in shock as she realizes why the metroids go berserk when they sense Zelda; her immensely strong life force, a result of her sealing power, would allow the metroids to rapidly mature into their adult stages. Her task finished, Samus drags the metroid carcass outside and incinerates it with her flamethrower and, hearing the screeches of many metroids, she rushes back to the ship. Upon entering, she explains to Link about what she discovered from the zeta metroid.

"So, what should we do about this?" Samus asks.

"Even though I don't like the idea of moving her around, it wouldn't be a smart idea to just leave her in one place either. We should just keep moving as a group, but if only there was a way to 'mask' her energy somehow…." Link ponders.

"Well, I might have a solution. I just need to reconfigure a device that I have. It will also have the added bonus of protecting her from phazon exposure."

"I'd like that." Link smiles. "Can you make it?"

"It'll be ready by the time we have to leave. Until then, you should get some rest. We'll be up bright and early." Samus walks over to her console to have the device prepared. Before this, she is stopped by Link.

"Listen, I'm sorry for what I said earlier. I was just angry at myself for being careless; I didn't mean to take it out on you."

Samus pauses before smiling. "It's alright. Everybody gets these moments from time to time. No one is perfect after all."

"Regardless, thank you for helping me out of my rut."

"Everyone needs help sometimes, even a superhero like you Link." Samus pats Links shoulder before returning to her console to prepare the device. Link pulls out a rollout bed and places it next to Zelda, mumbling to himself, "superhero, huh?" After a while, both of them fall asleep, Samus at her pilot seat.

* * *

 **The morning after. Zelda awoke to the sound of Link and Samus talking to each other, not catching most of it due to drowsiness. The chat ends with them shaking hands and then noticing that Zelda is awake.**

"Ah, good morning Zelda. You've been asleep for a while." Samus says as she walks up to her.

"Did you sleep well?" Link gently asks.

"I slept fine, I think." Zelda says before putting her palm on her forehead. "How long was I out?"

"Just evening yesterday until this morning. You handled yourself well against that metroid. How did you fight it off?" Samus asks.

"Urbosa taught me some swordplay whenever she had the chance. My father didn't like the idea of me picking up a sword, but she thought differently, so she taught me some basics without him knowing about it."

"A rebellious princess, huh? I like it." Samus crosses her arms and smiles.

"Easy for you to say, you weren't the one who had to see her 'rebellion' daily." Link quips, causing Zelda to playfully stick her tongue out at him.

"Alright, you two." Samus says as she lowers the blast shield on her cockpit. "Let's just get ready to head to the domain once again-" She cuts off as a blue glow enters from outside, they look out and see several blue tendrils across the wetlands, the water with a blue mist like shroud and several monsters roaming the area with piercing blue eyes and veins.

"What's happening?" Zelda asks with worry.

"It's the phazon. It's changing the ecosystem to suit its growth. This barrier is probably like a large bio dome to promote its development." Samus adds.

"This is bad…we need to get to the domain immediately." Link declares as he reequips his suit.

"Agreed. But first, you should get dressed, Zelda; I have a new device for you." Samus asks, earning surprise from Zelda as she reaches into the pack that has extra clothes that Link brought for the both of them. As she starts to pull off her robe, Zelda pauses as she and Samus stare at Link. Getting the message, he quickly turns around, apologizing for not giving her privacy, much to the two ladies laughter. Finally back in her usual attire, Samus hands Zelda a headband, broach, elbow guards and leg guards, each one with a single pulsating purple hexagonal plate. Intrigued, Zelda places each one in its designated area. Now, Samus instructs her to get near the hatch, causing Zelda to tilt her head in confusion, but does as instructed. Reacting to the phazon outside, an orange force field envelops her body, much to her surprise.

"Hazard shield active and fully functional." Virginia reports.

"Before you ask, this is meant to protect you from environmental dangers such as fire, electricity and even radiation. It also has the added effect of hiding your energy signature from the metroids; they won't be able to detect you anymore."

"Thank you, Samus." Zelda says while smiling, earning a nod from Samus.

"Now, I think we should head out to the domain."

Link, in response, places the master sword on his back and gives Zelda an ancient short sword recovered from the house. "Ready."

The trio exits the ship and makes their way back upriver, fighting off the occasional monster along the way. Now that Zelda was armed, fighting off the monsters was much quicker than before. Upon reaching Oren Bridge, they stop to hear a low growling sound. Going past some bushes, they spot an injured Lynel on the ground, which growls upon seeing them.

"What have we got here?" Samus questions while scanning the beast.

"No phazon detected on the creature. Subject is riddled with injuries, all of which are consistent with talons belonging to an Omega Metroid." Virginia reports.

"What's an omega metroid?" Link asks.

"The adult stage of a regular metroids life cycle. It's actually around the same size as our man-beast friend here. Speaking of which; what should we do with it?"

"I know." Zelda responds before kneeling down next to the Lynel and, using her power, begins to heal its wounds.

"Hey! What are you doing?!" Link shouts in alarm.

"He can barely move, we can't just leave him to die." Zelda retorts while Samus looks on with intrigue.

"But it's a Lynel; he'll attack us!"

"Link, we can't just leave him to die. We all have a common enemy; and it's those creatures. I'm sure he understands that at least." As she says this, the Lynel stares at her intently.

"But…"

"You trust me enough to come along with you on this journey and you even gave me a weapon. Can't you trust me enough to do this?"

Before he can answer, the Lynel stands up, surprising the three. Realizing that its injuries are, for the most part, healed, the Lynel picks up its weapons and then stares at Zelda. While Link and Samus ready for an attack, the Lynel, surprisingly, nods at Zelda and then runs off, leaving the group stunned.

"You see? I knew it would recognize that we were no threat to it."

"Hmm." Link drops his guard and decides to keep moving. Samus, on the other hand, remains speechless by Zelda's selflessness in helping a creature which would normally be an enemy, instead of finishing it off. Several minutes later, they reach the entrance to Zoras Domain.

* * *

 **Zora's Domain, the Great Zora Bridge.**

"Finally, there it is." Zelda breathes a sigh of relief.

"Alright, you two, here's how it's going to work; we're going straight in, stay alert at all times, destroy any phazon afflicted creature or metroid and above all, don't stray from the path. Clear?" Samus concludes and the pair nod. "Alright. Now, where is this divine beast located?"

"It's in Toto Lake, above and behind the domain." Link states while pointing in its direction.

"Hmm." Thinking it through, Samus consults her map of the area. "I think Upland Zorana to the west would be our best bet to reach the lake. To climb the rocky areas, you'll just hold on to my arms and I'll jump on the ledges."

Agreeing to the plan, the three move across the Great Zora Bridge into the domain, taking note of all the viscous fluid on the floor, stairways and pillars. A few steps inside and they hear rumbling underneath them, Link and Samus nod at each other and prepare their weapons with Zelda following their lead and drawing her sword. As expected, two large phazon tentacles erupt from the left and right of the bridge, releasing bokoblins and lizalfos upon them.

"Corrupted!" Link shouts while slashing at a bokoblin. Samus, in response, fires several power beam shots at the incoming monsters, but is restrained by the lizalfos tongues on both of her arms. Just then, one of them is immediately decapitated and the attacker is revealed to be Zelda. Samus nods at her and propels the other lizalfos towards herself and blasts it with her dark beam, point blank. Link fires bomb arrows in an attempt to stem the tide of attacking monsters before switching back to his sword and killing the bokoblins one by one; he slashes downward on one, moves on to the next slashes diagonally upwards. A lizalfos tries to blindside him from the right, but he shield bashes it away then follows up with thrust to its abdomen. Another lizalfos rushes towards him, but Zelda runs up, blocks its spear and runs the sword through its head. Now back to back, they become surrounded by the monsters.

"You two; hang on to something grounded!" Samus shouts and Link responds by driving the master sword into the ground and, with his free hand, holds on to Zelda. Samus, using the dark beam once again, fires a small purple-black orb that travels behind the monsters and expands into a small black hole, sucking the monsters in (Darkburst). After a few seconds, the black hole dissipates and the pair look back to see that a decent number of monsters have been eliminated. Their astonishment is short lived as more of the monsters charge at them.

"We're so close! Let's finish this!" Link shouts as he readies a skyward strike. Before he can unleash it, a loud roar interrupts the fight. The monsters look towards the domain before running away in fear. Confused, the group looks back at the domain.

"What was that?" Zelda comments.

"It's an Omega Metroid." Samus answers while arming herself. "That's the former apex predator from SR388. Be on your guard."

From the interior of the domain, two zeta metroids crawl out to meet the group, hissing all the while.

"Which one is the omega metroid?" Link asks while readying himself. As if to answer, thundering footsteps are heard behind the two metroids, growing in intensity as they come closer. From the shadows, a large reptilian like creature emerges, around double the size of the zeta metroids, with long arms ending in two fingered talons, a long tail, green spine-like armor on its back, five red eyes on each side of its head and a thick rib-cage coating protecting its nucleus.

" _That's_ the omega metroid." Samus confirms while taking aim. The omega responds by roaring, signaling the two zetas to charge. One of them tackles Samus to the ground and the other engages Link and Zelda. The zeta menacingly circles the pair, its mouth twitching as it waits to sink its teeth into them.

"Be careful Link; these creatures are very agile."

"Got it. Stay close to me." Link says as the zeta shoots a green bolt of energy, which they dodge to the right. Zelda manages to slash its back, leaving a cut on its carapace. It responds by swinging its tail, knocking her back and rushing at Link. He tries to stab its nucleus, but it overpowers him and drives him to the ground, leaving a large claw mark on his on his chest armor. It tries to bite down on his helmet, but Link holds it back with his left arm and punches its head with his right, which it responds by driving the claws on its left leg into his own, only protected by the quickly weakening armor that he wears. Getting up, Zelda sees Link struggling with the zeta, grabs his ancient bow, runs to the nearby shop and grabs a bundle of ice arrows (while mumbling 'they can bill me later') and shoots one at the zetas side, causing it to roll off of Link and attempt to pull off the arrow. Link gets up and slashes it across its nucleus, making it fall to the ground and he walks off. Zelda runs towards him and notices the zeta trying to attack him from behind. She hurries and runs her sword through its mouth and out the back of its head, finally killing it.

"Thanks." Link says while out of breath.

"No problem." Zelda responds reassuringly.

Meanwhile, Samus pushes the zeta off of herself and parries its lunges, making it fall on its back and then she shoots several missiles at its nucleus, ending its life. Afterwards, she shouts at the two to get down; they duck down as a red stream of energy flies above them, originating from the omega metroid.

"So, that's what was firing at us from the wetlands!" Link shouts as he stands up.

"Yes, it was guarding this area." Zelda comments while readying herself.

The omega charges at them, Samus fires a missile at it, but it lowers its head and the missile explodes harmlessly on its carapace. With its brute strength, the omega rams Samus against a pillar, disorienting her, and Link jumps on its back, holding its head up as Zelda slashes at its nucleus. However, its rib-cage like shielding prevents her from harming it.

"It's too hard!" Zelda shouts amidst the omegas increasingly angry roars. Finally, the omega tosses Link over its shoulder and gears up to shoot another stream at the ground and Link grabs Zelda to move them out of the way. Grabbing his bow, Link shoots a bomb arrow, slightly damaging its shielding and angering the omega.

"That's it! Keep hitting its shielding, you'll expose the nucleus!" Samus shouts while offering suppressing fire. Zelda uses her power to try and hold it back, but becomes surprised when her hands glow from golden to red.

"What is this- ahh!" The omega brings its fists down as she avoids being crushed. Link lets loose another bomb arrow, finally cracking its shield and exposing its nucleus. Desperate, the omega lunges at the pair as Link shield bashes its head, stunning it and giving Zelda ample time to slide under it and pierce its nucleus. The omega roars as it falls over backwards, croaking its last breaths. As the pair walks away, the omega suddenly regains consciousness, tail swipes Link away, then grabs Zelda and holds her aloft. Zelda holds on to the omegas muzzle to keep it from biting her until suddenly it roars in pain as her hands glow red once again, revealing them to be red hot. Before she can process what's happening, Samus rolls forward and shoots the omegas nucleus causing it to drop Zelda (who Samus swiftly catches) and Link delivers a horizontal slash, splitting the nucleus in half and finally killing the omega as it pathetically drops to the ground.

"Ok, that wasn't easy." Link says breathlessly. "Also, there was more than one of the blasts back at the wetlands. I take it that means that there are more of those?"

"Yeah, we should be very careful." Samus then scans the area and is shocked to see several hundred oval shapes in the domain and the cliffs surrounding it. "Link, do you see all of that?"

"See what?" Samus activates the organic detector on Links helmet as he sees the shapes as well. She does the same thing with Zelda, which appears as a monocle like apparatus from her headband.

"What are those things?" Link quietly asks as Samus responds; "Metroid eggs."

"There's so many of them…" Zelda says with astonishment.

"Now we know why the metroids were so desperate to keep us out; this is their nest." Samus begins calculating the probabilities of destroying the eggs. Virginia concludes that she'll lose power before freezing all of them and fighting off the attacking metroids, as well as estimating that the eggs will all hatch in about 3 hours.

"We'll worry about this later, for now we need to get to Vah Ruta." Link comments as they push on to Upland Zorana. Upon reaching the cliffside, Samus holds on to the pair and jumps up the cliffside and landing on the upland, they see several metroid eggs on the ground. Looking towards Toto Lake, Vah Ruta is seen glowing blue with several splotches of the same color all over it and its trunk pointed upward, releasing a glowing blue beam into the barrier.

Samus steps up to scan it from afar. "Now, that is one big elephant." Scanning Vah Ruta shows that it is releasing phazon which is powering the barrier, concluding that purging the phazon from the divine beast would remove said barrier.

"So, Vah Ruta is causing all of this." Zelda quietly adds.

"I stopped it once, I can do it again." Link determinedly proclaims.

"I hate to interrupt, but there are 3 Omega Metroids in Vah Ruta's immediate vicinity." Virginia reports to the group.

"And which way are they headed?"

"That's the thing; they're not moving at all, they're standing in front of it. It is as if they're protecting it."

Concerned, the group head towards Toto Lake, only to be spotted by a Gamma Metroid which then begins calling out. The call brings an assortment of larval, alpha, gamma and zeta metroids from their hiding places (behind small hills, in the grass, camouflaged on mossy walls, etc.), as well as an omega metroid barreling in through the trees.

"There's too many of them! What do we do now?!" Link shouts in alarm.

"I'm thinking, I'm thinking…" Samus answers, the worry present in her voice.

"Vah Ruta is in our sights, we need to do something!" Zelda shouts in worry while wielding her sword. The next thing they see is an ice arrow strike an alpha metroid, killing it and spreading ice at three larval metroids surrounding it. The group turns around to see none other than Sidon, holding a silver bow.

"Then just leave everything to us, princess." Sidon smiles as a group of zoras, including King Dorephan (holding a larger than average silver longsword) and Muzu (holding a silverscale spear), appear from behind him, having swam up the Veiled Falls. "We will not stand idly by as you fight our battles. We are here to reclaim our home from these beasts!"

"I think the odds are tipped in our favor." Link confidently says while smiling.

"Soldiers! Open a path for our friends!" Sidon shouts as the Zora soldiers charge forward with spears and swords ready, attacking the besieging metroids. Two guards escort the trio past the fighting, however they don't get very far before being intercepted by two gamma metroids. They shout at them to run before engaging their foes. Reluctantly, they run for the lake as Sidon shouts that the omega is about to intercept them. Samus prepares to shoot at the incoming omega, but to their shock, it is tackled by a Lynel and tossed against a wall. The Lynel roars at the omega, which shakes off the impact and furiously roars at it in response. Zelda realizes that it is the same Lynel she helped earlier, which then looks at her briefly before tossing its bow at her feet, which she picks up. Understanding its intentions, they continue towards Toto Lake as the Lynel and Omega Metroid charge and collide with each other and begin to fight.

"I admit it, you helping that Lynel was a great idea." Link speaks up.

"I told you; we have a common enemy." Zelda responds. "I just hope we can restore Vah Ruta before they lose too many people…"

"We'll make it. We _have_ to." Samus sternly retorts. "Come on! It's just over these hills!"

The three begin to run even quicker, determined to stop the metroids once and for all.

* * *

 **At Toto Lake, the 3 omega metroids stand in front of Vah Ruta, growling and snarling as they await the trio to approach. From the lake and underneath Vah Ruta, the water bubbles unsettlingly as growls are heard from beneath it…**

 _To be continued._

* * *

 **Author's note: Well, there you have it; they finally reached the divine beast! Now, I should point out that, according to the Hyrule compendium in BotW, Lynels are known for being intelligent unlike the other monsters, which is why I took the idea of having an injured Lynel aided by the heroes that would then help them in return. Now then, I'm off to start the next chapter (I don't know when it will be done, because I don't have an actual schedule, heheh) and once again; rate and review please! :)**


	9. Chapter 9 The Queen Guardian

**Chapter 9: The Queen Guardian**

"Let us not burthen our remembrance with a heaviness that's gone." -William Shakespeare

 **The Zoras continue to fight off the besieging metroids, buying the trio as much time as they can to restore Vah Ruta and halt the spread of corruption.**

"Don't let up, we have to hold them off for as long as we can!" King Dorephan declares while swinging his sword, bifurcating several gamma metroids. "Muzu, are you alright?"

Muzu, albeit with some difficulty given his age, swings his spear in a manner that catches several larval metroids off guard. "Hah! This is how we did it back in the day, your highness!" Muzu then kicks away an incoming alpha metroid. "It would bring shame to lady Mipha if her teacher didn't live up to expectations."

King Dorephan smiles widely at his old friend's determination as they both continue fighting alongside their warriors (surprisingly, Sidon is nowhere to be found).

* * *

 **Toto Lake**

Finally having arrived at the lake, the three bear witness to Vah Ruta's corruption, even covering the water surrounding it (the ruins having been previously cleared and the lake being expanded to allow Vah Ruta to be stored in it).

"Remember; there are three omega metroids protecting the divine beast. Keep your guard up." Samus reminds the pair as those same three come into view, growling and snarling at them.

"Speak of the devil." Link says while gripping the master sword tightly. "Let's clear them out and head inside the divine beast."

Suddenly, an alarm goes off inside of Samus's suit. "Warning; there is another metroid signature coming from underneath the divine beast." Virginia confirms, alerting the group.

"A fourth omega metroid perhaps?" Zelda questions.

"I'm afraid not; it is a category 5 metroid."

Samus becomes unnerved by this, and berates herself for not realizing the obvious of where the eggs came from, at first assuming that they were produced solely by the phazon.

"Samus, what is a category 5? I thought the omegas were the last stage of development." Link addresses this inconsistency with dread.

"Not entirely, there is another stage, but it is a rare occurrence. Few metroids have the genetic capacity to develop into this form and they're the ones who lay the eggs." Samus answers and as if to confirm it, the omegas step aside as a massive beast with an armored carapace, four large three toed legs, an extendable neck, 6 pairs of eyes, a mouth resembling more of a crocodile instead of a leech with an additional jaw flap on each side of its head and a long tail with a dorsal tube on each side of its rear. "They are known as Queen Metroids." The queen then roars at the intruders, causing a slight tremor as it does, followed by a massive stream of red energy fired from its mouth at the group. Link jumps in front of Samus and Zelda, hits his knuckles and then extends his arms outwards as the burst hits them. When the dust finally clears, an orange force field surrounds the group, protecting them from the blast.

"What just happened?" Samus, with genuine confusion, asks.

"It's Daruk's Protection." Zelda answers, a hint of nostalgia present in her voice. "Link was given this ability by the Goron champion of the same name."

Link then dispels the barrier and prepares to fight as the queen commands the omegas to attack. "Here they come!"

Link blocks one of the omegas as it pushes him back. Before they can come to his aid, Samus and Zelda are intercepted by the other two. Zelda, using her power like a makeshift barrier, manages to toss one of the metroids behind them just as the other runs up and is hit by Samus' ice beam, causing it to run about and try to get the ice off. While this is happening, Link continues to struggle with his omega, until an automated voice in his suit speaks to him, **"Structural integrity of omega metroid analyzed, Augmented Kinetic Energy Burst (AKEB) online."** As the voice concludes, the master sword vibrates intensely while radiating glowing purple energy. Not thinking twice, Link slashes at the omegas ribcage shielding, causing it to be blown backwards and then falling on its side with its shielding broken and having received significant damage as it tries to stand up.

"Now that's what I'm talking about." Link smiles as he observes the sword as it returns to its regular state.

"Link, you have another omega rushing towards you on your left! Get out of the way!" Samus shouts as Link looks to his left and sees an omega metroid running at him with its mouth wide open, roaring all the while. Seeing this, Link grips the hilt tightly with both hands to activate the AKEB (AKEB: **charging…** the sword is quickly imbued with kinetic energy, giving it the characteristic purple glow and vibration **...charge complete** ) and upon completion, quickly runs forward and slashes vertically at the incoming omega metroid. Recovering from the slash and behind the metroid, Link sees that the power released from his attack split the metroid vertically in half (from its mouth to the tip of its tail). "That's one less to worry about." Link breathlessly comments, also realizing that the AKEB causes fatigue if used frequently.

Angered by its childs death, the Queen roars loudly causing everyone to lose balance as it fires a large stream of energy at Link (which he manages to avoid). It then enters the fight and before Link can engage it, the omega that he fought previously gets back up and begins screeching and stomping the ground. Finally, the metroids red eyes turn blue and its body radiates phazon energy (complete with wiggling blue tendrils), confirming that it entered hypermode.

"Oh, not good…" Link worriedly says and before he can ready himself, the now faster omega metroid smashes into him, sending Link back a good distance onto his back.

Seeing this, Zelda and Samus try to rush to his aid, only to be intercepted by the other surviving metroid (also activated hypermode). "Get out of the way!" Samus tries to aim at the metroid, but is quickly grabbed and thrown onto the ground with a resounding thud. The metroid holds her down with its arm and fires a powerful stream of phazon while she's pinned down. "AAAHHH!"

"Shield damage, reaching 45% of shielding threshold." Virginia reports.

"LET HER GO!" Zelda shouts as she tries to summon her power, but the metroid swings its tail at her, sending Zelda back 3 feet.

"Zelda!" Samus shouts amidst the metroids furious attack.

"Reaching 75% of shielding threshold."

Disoriented, Zelda stands up and once again tries to summon her power to at least stun the metroid, but the impact of the metroids tail whip continues to affect her. "Come on, I need this power now!" Zelda tries once again to use her power, but to no avail. She soon becomes distracted by the scene in front of her; Link mercilessly beaten by an omega and the Queen (tossed around by the leg, the queen ramming her head on him, receiving a green bolt of energy from the omega, etc.), only being more or less protected by his already damaged suit and Samus screaming as she's hit by a constant barrage of phazon energy. All of this culminates in Zelda feeling total despair as she remembers how her father, the champions and the people were slaughtered before her and she was powerless to stop it, now she's about to feel it all over again. "No…" The triforce mark on her right hand begins to glow. "No!" Her aura switches from gold to red. "STOP!" In anger, she extends her palm forward at the omega, the mark on her hand changing from the triforce to the symbol of the goddess Din, and shoots a large fireball at the metroid. Upon impact, the omega is thrown from on top of Samus and onto the ground. Samus looks to the side and is surprised to see Zelda radiating this strange power.

"What is this?" Samus asks, visibly weakened by the attack as she tries to stand up.

"I can hear it, a voice in my head saying: Din's Fire." Zelda answers, but realizes that the metroid stands up again, a large burn mark present on the right side of its abdomen, which then causes it to roar in anger. "Samus, just rest for now, I'll handle the metroid." Undeterred, Zelda continues to maintain the power of Din's Fire and stares at the metroid, ready to face it. "I've been at the mercy of monsters like you; never again." Zelda launches another fireball, catching the metroid off guard and receiving another blow, this time at its head. Continuing the barrage of fireballs, Zelda manages to force it back as it screeches in frustration, unable to counter attack the fireballs. Although initially having the upper hand in the fight, Zelda quickly discovered a drawback to Din's Fire; overuse of it causes fatigue, which begins to affect her. Finally, Zelda brandishes the ancient short sword and imbues it with fire and before the metroid can retaliate, she runs up and slams it down on its chest, causing it to screech in pain and destroying her sword. The impact sends them both a few feet back in opposite directions. Getting on her back, Zelda breathes heavily, trying to calm the headache brought on by her magic. Her recovery is short lived as the heavily injured omega metroid walks up and looms above her, growling angrily. Zelda pulls out her bow (given by the Lynel) and aims an ice arrow at it. "I am not afraid of you…"

The metroid moves in to bite down on her, but her broken sword gets driven through its left shoulder. Groaning weakly, the metroid is forced away from her direction and, to Zelda's surprise, it is revealed to be Samus. She then jams her left hand and elbow to keep the metroids mouth open as she finishes charging her cannon. "Bite this." Samus runs her cannon into the metroids mouth and blasts her ice spreader inside, rupturing its nucleus from the inside out and shattering its frozen head as the metroids corpse falls to the ground. Wearily, Samus walks over to Zelda and offers her hand, which she gladly accepts. "You've got a lot of backbone, I'm impressed." Samus says while smiling.

"Not bad for a rebellious princess, right?" Zelda quips, but she remembers that Link is still being attacked. "Samus, we have go help Link!" Nodding to Zelda's statement, they both make a beeline for Link.

Back at the Queen and remaining Omega, Link is pinned to the ground by the queen as the omega looks on. Unable to get up, Link fruitlessly tries to reach for the master sword, only mere inches away from his hand. As the queen moves to bite down on Link, she is interrupted as a trio of bomb arrows knocks away the omega metroid. She looks to the direction of the arrows, followed by Link, Zelda and Samus (still a small distance away) and they both see none other than Sidon running towards them.

"Hold on Link!" Sidon jumps and vaults off of the stunned metroid onto the Queens back, stabbing its back with the trident to keep from falling off and causing the queen to shake violently to get him off. The metroid stands back up and before it can fire at Sidon, Link slams his charged sword into the metroid, interrupting its attack. Sidon notices this and sees Link covered in a water-like shroud with a transparent silhouette of Mipha floating around him and restoring him to full health. "Sister?"

The Queen takes advantage of Sidon's lax in attention and manages to shake him off. As he gets up, the omega readies to slash at him, but is hit by a salvo of missiles and two ice arrows at its nucleus, which Sidon sees the chance to slam his trident into it and shattering the nucleus. The metroid falls to the ground, exhaling its last breath as the Queen recomposes itself, its anger increasing by the death of its children.

"Thank you for the help." Sidon says to both Samus and Zelda, who in turn nod at him.

"You showed up at the best time, I was getting worried." Link says to Sidon, who grins widely at him.

"So this is the beast responsible for the metroids?" Sidon says as he looks at the Queen. "It's bigger than I thought."

"Yes, it's the one that laid the eggs around the domain." Zelda confirms while arming her bow.

"But, if we face it together, we should be able to stop it before the eggs hatch." Samus states while activating the ice beam. A small counter appears at the top of her visor: **one hour and 43 minutes remain before the eggs hatch.**

"So what do you say, Sidon? You up for another round to appease Vah Ruta?" Link asks while readying himself.

"I thought you'd never ask." Sidon proudly responds as the four ready themselves to face the queen metroid, who then roars at them, ready to attack.

* * *

Back at Upland Zorana, the zoras have managed to quell much of the metroids, though not without casualties. The injured are precariously dragged off of the battlefield to be attended by the healers, risking attack by the metroids. King Dorephan himself having received several injuries nevertheless keeps on fighting the beasts.

"My king, you should pull back. Your wounds need healing." Muzu, who is also injured, says. "We'll handle the metroids."

"I don't have time to heal, we must all do our part Muzu, and you know that." King Dorephan replies, unwilling to let his people fight alone.

As he says this, Muzu looks behind them to see the remaining soldiers, both healthy and injured, ready to continue fighting. Muzu, with eyes watering, points his spear at the metroids.

"You heard your king! Forward!" Muzu declares, earning shouts of acknowledgment as they charge at the metroids once again. On another side of the fight, the Lynel (with several scratches and bites) continues fighting the omega metroid. With its sword knocked away, the Lynel resorts to fighting it bare handed, grabbing it by the throat as it lunges. Slashing at its chest, the Omega releases itself from the Lynels grasp and, using its tail, tosses it against the wall, disorienting the Lynel. The Omega fires a stream of energy and the Lynel counters by shooting a fireball to cancel it out, causing a smokescreen. The smoke clears and the Lynel is nowhere to be seen, the Omega turns around just in time to see the Lynel, with its sword retrieved, running towards it and before it can react, the Lynel decapitates the Omega from the from the top jaw down. Placing one of its legs on the metroids corpse, the Lynel roars triumphantly before running off to attack the other metroids.

* * *

Back at Toto Lake, the group continues fighting the Queen Metroid with little results against it hard carapace, until Link gets an idea; using the Sheikah Slate, he throws a remote bomb as it opens its mouth and as it reaches the nucleus, he detonates it. Stunned by the contained explosions, the Queen falls to its side, giving everyone ample opportunity to attack its now exposed nucleus which they all take(Link releasing a flurry of slashes, Zelda shooting three ice arrows at once, Sidon initiating a flurry of thrust with his trident and Samus firing several ice beam shots). Soon however, the Queen recovers, gets back up and slams its tail at all four of them. The first one to recover from the hit is Samus, who tries to damage the Queen, but is blasted against the wall by its energy stream. Getting up, Link notices an announcement from his suit: **AKEB is back online and ready to use.**

"I've got it; Zelda, Sidon, cam you guys keep her distracted? I've got a plan to end this."

"Leave it to me." Zelda says while radiating her power.

"I'll buy you as much time as I can." Sidon says with determination.

From the wall, Samus curls up into a ball and then boosts onto the Queens head and ricochets off of it and back on the ground. "Count me in!"

Link charges a skyward strike and launches it at the Queens head, destroying three of its eyes. The Queen howls in pain as Link gives them the signal to distract it and he charges the AKEB. Fully charged, Link looks for an opportunity to attack until his suit alerts him, **Warning; Kinetic energy critical, 25 seconds until AKEB automatically releases energy to prevent damage to the user and weaponry.** "You've got to be kidding me!"

Seeing no alternative, Link rushes through his friends that are providing cover fire and prepares to land a blow on the Queens head, but with its remaining eyesight it shoots a green bolt of energy square on Links chest, sending him back and dropping the charged master sword. **20 seconds remaining.** The Queen attempts to attack, but Samus jumps in front of it, keeps its mouth open with her feet and left arm and shoots ice down its mouth, causing it roar and violently thrash about. **15 seconds remaining.** Zelda keeps it in place with her power and Sidon stabs his trident into its nucleus.

"Link! I don't how much longer we can hold her! Whatever you're planning, do it now!" Zelda shouts, struggling to keep the Queen from moving.

"It's your show, Link. Make it a good one!" Samus declares, struggling to keep the Queens mouth open.

"This is the final push, Link. I'll always believe in you!" Sidon proudly shouts, inflicting as much damage as he can.

Link recomposes himself and reaches for the sword. The now enraged Queen activates hypermode, blasts Samus out of her mouth, kicks Sidon away and swings its tail at Zelda and fires several phazon blasts at Link. **10 seconds remaining.** Link uses his shield to parry several of the blasts away, being pushed back a few inches with each hit. Undaunted, Link pushes forward, now with his shield acting as a barrier against a now constant stream of phazon energy from the Queen. **5 seconds remaining.** The Queen continues its onslaught as Link buckles under the pressure. **FOUR.** A fireball then hits the Queen on the side of its head, interrupting its attack.

"Now's your chance!" Zelda shouts in desperation. **THREE.**

"RAAAHHH!" Link charges forward with the sword ready as the Queen lunges to grab him in its jaws. **TWO.** Link thrusts forward as the Queen bites down on him, earning shock from the others.

 **ONE.** The Master Sword erupts from the top of the Queens head, releasing the kinetic energy. The Queen roars in agony as Link, with slight injuries, hangs from her mouth before removing the sword and falling to the ground. The Queen shakes around and screeches in pain before letting out a final howl as it falls to the ground and exhales its last breath.

Link sits up and sheaths master sword, but falls back down, utterly exhausted. The next thing he sees is Sidon standing over him, offering his hand while smiling.

"I knew you'd never let us down." Sidon comments. Link smiles proudly and accepts his hand. Standing him up, Sidon pats Links shoulders in happiness. Zelda walks up to them with Samus on her left shoulder (the latter having deactivated her suit to ease the burden on Zelda).

"You never cease to impress me, Link." Samus says while extending her hand to him and smiling.

"Well, we couldn't have done it alone." Link kindly says as he shakes her hand. He then turns to Zelda. "Since when could you shoot fire? I had no idea."

"Since just now. I think it's derived from my power. I didn't know it was possible either." Zelda says, unsure of its origin.

"Well, I'm glad you have a new means of defending yourself. But, maybe I should also teach you how to fight as well, what do you say to that?" Link says, smiling all the while.

"Really?!" Zeldas beams ecstatically, happy that Link would finally teach her something that he was originally opposed to back in the day. "I'd love to!"

"But first, we should get you a new sword…" Link stares at the broken ancient short sword hanging from her hip.

"Actually, the first thing should be that." Samus points to the still corrupted divine beast. They all nod in agreement and walk towards Vah Ruta; Samus reactivates her suit and freezes a path towards it to avoid the phazon infected water.

* * *

 **Inside Divine Beast Vah Ruta**

Link leads them to Vah Ruta's main control unit, which is covered in phazon.

"My goodness, this is extraordinary." Samus marvels at the inside of Vah Ruta and its complex machinery. But, she decides to put it off for later and restore Vah Ruta. "Now then, I just need to add the vaccine to the main control unit and the phazon should be purged. Here goes." The muzzle of her arm cannon opens up into four flaps, which she places on the console. The vaccine begins its administration, but is abruptly stopped. "What's going on?"

"Samus, there is insufficient power to administer the vaccine. Even at 100%, it would still not be enough for a machine this massive." Virginia reports, earning a disapproving scoff from Samus.

"Samus, what's wrong?" Zelda asks with concern.

"There's not enough power to administer the vaccine. I can't fix it…"

Everyone becomes discouraged by the news and begin to worry about how they can bring down the barrier, until Zelda speaks up.

"The problem is that you need more power, right? More than you can actually give?" Zelda asks, earning a nod from Samus, who is looking down on the console in frustration. Zelda, with her index finger on her chin, ponders an idea. "Then, I wonder…" Zelda summons her power and transfers it to Samus.

"What are you doing?!" Samus asks in alarm as she is bombarded by massive amounts of power. Zelda stops and before she falls down, Link catches her. Samus then notices that her visor and lights on her suit have changed from green to gold. "What is this?"

"Power levels at 400% capacity." Virginia reports.

"Is that enough?" Zelda breathlessly asks while Samus looks at her with surprise.

"More than enough... Alright, let's try again." Samus turns back to the console and administers the vaccine once again. Sure enough, it begins to purge the phazon from the divine beast. The others stare in awe as the phazon tendrils disappear and the divine beast regains its former glory. From outside the barrier surrounding the Lanayru, Hateno and Kakariko regions disappears. The Zoras and Lynel, having repelled the metroids, bear witness to this and erupt in thunderous applause. Samus removes her cannon and notices that her former shine returned, having drained all the power that Zelda gave her.

"Vaccination complete. Vah Ruta is freed from further corruption." Virginia confirms as everyone breathes a sigh of relief. Just then, an ethereal green light appears behind them. Sidon becomes shocked at seeing the spiritual form of Mipha smiling at them.

"Hello Sidon. I have missed you."

"Mipha? How can this be?" Sidon asks in disbelief. "Is it really you?"

"It is me, little brother." Mipha says with a warm smile as she spreads her arms out. Sidon, with tears in his eyes walks over to embrace his sister, whom of which is now shorter than him.

"I-I thought I'd know what to say if I ever saw you again, but now I can't even find the words anymore." Sidon holds on even tighter as he loses breath in between words. "I can't believe it."

"Dear Sidon, you have become an exemplary Zora. Just as I knew you would." Mipha says as Sidon loosens his grip, allowing her to face the others. "Samus Aran, we finally meet."

"You know my name?" Samus asks in surprise. "How?"

"An old friend told me." Mipha explains and Samus realizes who she's talking about; King Rhoam. "Now, I thank you for aiding my people. Your heart is noble and your spirit is strong." Mipha says this as she courtesies.

"Thank you for your kind words, but I'm just a bounty hunter. Hardly worth the word noble."

Mipha gives Samus a compassionate smile before continuing. "I think otherwise, you've come to help us, yet I haven't heard you ask for any form of compensation. I believe you are indeed noble." Mipha corrects Samus, who in turn looks to the side. Mipha then looks at Link. "Link, I thank you for helping to free Vah Ruta once again."

Link, feeling a sense of guilt, doesn't even look her in the eye. "Of course, I'd...never let you down." Mipha then looks at Zelda and smiles.

"Princess Zelda, it is good to see you again after all this time."

"Mipha, my friend. I thought I'd never see you again." Zelda says, also teary eyed. "But, how are you here?"

"The goddess Hylia has allowed me the time to bring you this message; Hyrule is once again in need of their champions in this time of darkness."

"We need to find new champions for the divine beasts?" Link asks.

"Yes. But, they can't be just anyone. They must have all the traits of the previous champions before them. And they must be anointed by you and the princess. Only you can see who is worthy of the mantle of champion."

"This is very sudden. How will we find a new champion for Vah Ruta?" Zelda wonders aloud.

"I don't think we have to look very far." Link says. "First off, let's describe Mipha's personality; she's kind, loyal, a beloved friend and fiercely dedicated to the protection of her people." Mipha blushes at these words while fidgeting with her hands. "I know one other person who shares these traits; Sidon."

"Me? But, I'm just the brother of the previous champion. I can't compare to her in any way." Sidon counters Link's statement with downcast eyes. "I'm not worthy of being called a champion."

"Neither was I." Link cuts in. "I only planned to be a soldier of the army and becoming a champion was the furthest thing from my mind. But, I was called upon to become the champion of Hyrule. From then on I knew; it's our destiny to be greater than we already are. Let no one, not even ourselves, tell us who we can or can't be." Link declares while handing Sidon the lightscale trident once again (having dropped it previously when he was reunited with Mipha), as Zelda, Mipha and Samus smile at his declaration. Sidon takes the trident, pauses for a few seconds and gives Link a determined smile and nods. Link does the same before turning to Zelda, who gets the message and turns to Mipha.

"Gentle Mipha, I hereby appoint Sidon, crown prince of the Zoras, the champion of Divine Beast Vah Ruta." Zelda proudly declares.

"Princess Zelda, I wouldn't have it any other way." Mipha accepts the decision and then walks towards her brother. "Sidon, I asked you to be the protector of our people and you have done so much more. You are now the champion of Vah Ruta, champion of the Zoras. I couldn't be more proud of you." As she says this, a blue sash wraps around Sidon's waist, bearing the symbol of Vah Ruta. "Now, my dear brother, continue being the strong protector of Zora's Domain. I believe in you."

In response, Sidon flexes his right arm and gives her a sharp toothed smile. Samus is then alerted by Virginia.

"Forgive the interruption, but there is still the matter of the metroid eggs in the domain. They will all hatch in roughly 17 minutes." Virginia confirms and before anyone can panic, Sidon steps up.

"Leave that to me. Vah Ruta is capable of producing heavy rain across the region and last time I checked, those metroids can't handle the cold." Sidon declares. "So then Link, come with me." Both Sidon and Link walk up to the main control unit and Sidon prepares to have Vah Ruta start heavy rainfall. "Link, do you have any way of forming ice?"

"I have this, will it be enough?" Link pulls out the master sword and, with the suits capabilities, imbues it with ice. Sidon nods and, using the wisdom passed on from Mipha, commands Vah Ruta to begin. Vah Ruta trumpets loudly and produces a deluge of heavy rain.

"Now, I hope they don't mind that it will get a little nippy outside. Link, lodge the sword into the main control unit, now!" Link does as he is told and, incredibly, the rain turns into freezing rain. Across the region, the metroids succumb to the freezing rain and fall to the ground, never to rise again. The Zoras then bear witness to the hundreds of eggs cracking and crumbling from the cold, ending the threat at last.

"And...That should do it." Sidon commands Vah Ruta to stop the rain and Link removes the master sword.

"No more metroids detected and all eggs have been destroyed." Virginia confirms much to Samus's complete shock.

"Incredible...this is the power of the Divine Beast?"

"That's why they're called mechanical wonders." Zelda giggles as she sees both Link and Sidon fist bumming and smiling. Now, their labors completed, the group decide to return to the domain and tell everyone the good news. Before that, Link tells everyone to go on ahead as he still has things to tell Mipha, who is residing within the divine beast until further notice.

"Mipha?" Link calls out and Mipha floats down from her perch atop the divine beast.

"Link? Is everything alright?" Mipha asks with genuine concern.

"I'm sorry, Mipha." Link remorsefully says as a confused Mipha looks on. "You and the other champions will always be important to me. But, try as I might, I can't remember our times together, not even with you." Link clenches his fists in frustration and shame before continuing. "I know how important the zora armor you left for me is and I know its significance. In another time, I think I'd be flattered and thought that you'd make a wonderful wife. But now, if I barely remember any of our times together then how could I ever be the man you thought I was?"

Saying nothing, Mipha walks up to Link and hugs him, much to his surprise. "Oh Link, it was never your fault that your memories were fragmented. There are things that cannot be changed, but one should always expect them. The past is in the past, so look to the future now." Mipha loosens her grip to look at Link in the eyes. "There are many trials and tribulations on the horizon, but I know that you will all pull through. The Princess needs you Link, protect her."

"I- of course." Link, feeling more or less eased of his burden, says to Mipha, who then kisses his cheek, much to his shock.

"And remember, even though your memories haven't returned, my soul belongs to you." Mipha then embraces Link once again, only this time Link returns the hug. After a few seconds, they separate and Mipha places her palm on his cheek and smiles warmly. "Go now."

Nodding, Link walks out of the divine beast and with a renewed sense of duty, runs off to Upland Zorana. Upon reaching it, he sees Zelda and Samus conversing with the Zoras, all of whom ecstatic that their home is safe once again, Sidon in particular crushing the two in a hug, much to Samus's mortification, Zelda's slight embarrassment and Link's laughter. They all then notice him and cheer for him, Zelda, Sidon and Samus in particular smile proudly at him. Link then realizes that Mipha was right in that they all should look towards a brighter future, free from the darkness that plagues the land. Something that he plans to do with the aid of everyone, fir true strength lies in unity. Link runs towards the group as Zelda runs towards him. Then, from out of nowhere, a blue meteor impacts Link and tosses him over the Uplands.

"AAAAHHH!" Link shouts as both he and the meteor impact the domain.

"LINK!" Zelda shouts in horror as the others run up to witness the event.

"What treachery is this?!" Sidon looks down to see a barrier covering the domain.

"Virginia, what's going on?!" Samus asks as Virginia scans the barrier, until she gives her report.

"Samus, it's her…" Virginia confirms as Samus reacts in horror.

"It can't be…"

"Samus?" Zelda asks as Samus reactivates her suit and runs down the Uplands, Zelda and the others follow her.

* * *

Link gets up off the ground, groaning from the impact. Recomposing himself, he sees that he's back in the domain which is now covered by a barrier.

"What's going on? What is this?" Link wonders aloud before being distracted by otherworldly sounds emanating from dust covering whatever it was that hit him. Link focuses his vision and as the dust clears, it is revealed to be Dark Samus slowly floating towards him. "Who are you?"

"I found you… prepare yourself…" Dark Samus menacingly whispers as she takes aim.

 _To be continued_

/_\

 **Author's note: *whistles* I think this might be the longest chapter I've written thus far. Anyway, I decided to do a small scene involving Link and Mipha because I didn't like very much how there wasn't enough interaction between him and the other champions, it just seemed like a missed opportunity to me for more character development. Nevertheless, stay tuned for the next chapter and once again, rating and reviews are most appreciated. :)**


	10. Chapter 10 The Fury of Dark Samus

**Chapter 10: The fury of Dark Samus**

" _Try to tear us apart, but know that we'll wear our scars. -I Prevail"_

Link gets up off the ground, groaning from the impact. Recomposing himself, he sees that he's back in the domain which is now covered by a barrier.

"What's going on? What is this?" Link wonders aloud before being distracted by otherworldly sounds emanating from dust covering whatever it was that hit him. Link focuses his vision and as the dust clears, it is revealed to be Dark Samus slowly floating towards him. "Who are you?"

"I found you… prepare yourself…" Dark Samus menacingly whispers as she takes aim. Moving fast, Link brings up his shield, defending him from the blast of phazon which pushes him towards the barrier, causing him slight injury.

"Wait a minute; you're the one I saw in Kakariko village!" Link says as he stands up right. "What do you want?!"

"Your world…" Dark Samus responds before rushing in and bashing Link with her right shoulder, causing him to fall to the ground and then aims at his head, looming over Link. "And your blood…"

Link quickly grabs her arm cannon and deviates her phazon stream away from him, then he kicks her away, jumps back to his feet and draws the master sword. In response, Dark Samus lunges forward with her cannon and fires a stream of phazon, which Link manages to split with his sword. He then dodges several shots while running forward. "This ends now!" Link severs Dark Samus's cannon and bifurcates her at the waist. His victory is short lived as he watches in horror as both halves of Dark Samus's body reconnect via tendrils erupting from the openings and then follows up by regrowing her arm cannon.

"No… it's just beginning…." Dark Samus maliciously laughs as her body reconstructs itself. Noticing that Samus, Zelda and the Zoras have arrived at the domain, Dark Samus looks at Link and brings up her left hand. "Now, let the carnage… BEGIN." She snaps her fingers, summoning the Yiga and several corrupted monsters.

"Men! Fight for our God's glory!" Silas, leading the Yiga, shouts as the footsoldiers storm the domain, attacking the battle weary Zoras.

"Get the elderly and the children out of here, now!" Sidon shouts before engaging a pair of blademasters. "Leave my home!"

Zelda attacks several bokoblins with a silver sword offered by one of the guards, along with her spells. She is nearly blindsided by a lizalfos, which is then blasted away by Samus. "Keep your eyes open! They're all over the place!"

"I know! There's just too many of them! They were brought on by that stranger in the dome with Link, weren't they?" Zelda asks.

"Yes, I'll explain who that is later. For now, we should secure the domain!" Samus explains before being cut off by a loud roar, revealed to be a corrupted blue Hinox running across the bridge to the domain.

"They brought a Hinox, of course…" Muzu, with an annoyed tone, speaks up.

"That thing's going to destroy the domain! We have to stop it!" One of the guards shouts, which Samus responds by running towards the Hinox and somersaulting at it while radiating energy and it simply swats her away, having been further strengthened by phazon corruption. Getting back to her feet, Samus lays down a hail of power beam shots at it. Zelda moves to shoot fireballs at the Hinox, but Samus stops her.

"I'll handle this monster! You worry about the others! "Samus orders as Zelda nods and returns to the others, silently praying that she makes it back.

* * *

 **Inside the dome**

Link continues his fight against Dark Samus, with the added desperation of being unable to help the others.

"Why do you insist on fighting…?" Dark Samus asks after firing a scattershot of phazon energy.

"Because I have many others depending on my success." Link answers while dispelling his now exhausted Daruk's Protection. "And my home has seen enough calamities already." Link then points around the domain with the master sword at both opposing forces. "Look around us! The people will continue to oppose you as long as they have the spirit to continue fighting."

Dark Samus looks around to see the Zoras, injured or not, fighting back against her forces. She then looks back at him. "You're right; these people have the will to fight against overwhelming odds…. But _he's_ about to change that…" Dark Samus then telepathically communicates to an unknown person. "Wreak havoc…" As she says this, dark storm clouds cover the sky and cause a heavy downpour.

"Fine, I'll do it myself." The stranger responds telepathically before taking flight from the cliffs overlooking the domain. Upon flying low enough, the stranger rains down a volley of fireballs at the zoras. They all look to the direction that the fireballs came from, but are unable to see the culprit due to the storm clouds and rain obscuring their sight. The stranger flies back down and fires a stream of superheated energy (while roaring).

"What is that thing?!" Link angrily shouts as he charges at Dark Samus, who parries his strike with her cannon and roundhouse kicks him to the barrier.

"Just a friend…" Dark Samus answers as she watches Link get back on his feet. "Now, I think our little game is at an end…" She takes aim at Link once again. "Die…"

Before Dark Samus can attack, Link lunges forward and slashes up her chest, causing Dark Samus to recoil and exclaim in pain. Looking forward, she notices the master sword covered in phazon, Link having previously coated it from the barrier. "A strength and a weakness in one. How embarrassing." Angered by Links mockery, Dark Samus charges again and forces him on the ground and, thinking quickly, he kicks her off and gets back on his feet. Dark Samus moves in to shoot him, but Link knocks her cannon away and then bashes her face ( **A/N:** Or visor, whichever you prefer) with the edge of his shield. He then lays down a flurry of slashes to her while she's disoriented and finishes the fight by running the master sword through her chest. Dark Samus falls to her knees and struggles to breathe as she bleeds out (phazon).

"It's over. We've won." Link calmly announces to his "vanquished" foe, only for Dark Samus to look up at him, her visor turning from bright blue to black.

"Not quite…" She responds before crumbling to bits. Link doesn't have time to ponder these words as he is blasted from behind by a burst of phazon. Recomposing himself, Link looks back to see Dark Samus, without a single bit of damage on her.

"How? I just destroyed you!"

"You simply destroyed my Echo… You didn't believe that it would be that easy, did you…?"

Link charges forward and attempts to slash at Dark Samus's head, which connects. To his horror, not even a dent was left on her helmet/head, the phazon having dissipated from his sword. Dark Samus sinisterly laughs before blasting off the master sword and the armor from Link's right arm (the sword landing a few feet away). Before Link can react, she grabs him by the collar and head-butts him three times, destroying his helmet, and then shoots him point blank in the abdomen, leaving another breach in his armor and causing him to kneel over. Shakily, Link gets back up, much to the surprise of his opponent.

"Still you stand…?" Dark Samus asks.

"Hah….This is nothing." Link defiantly answers while pondering a way to reach the sword quickly.

"Very well… No more holding back…" Dark Samus flies forward with her left hand outstretched.

* * *

The Zoras, not only attacked by the monsters and Yiga, are bombarded by several fireballs and superheated energy.

"Master Silas, our liege's ally has entered the fray." A Yiga footsoldier kneels beside Silas before addressing him.

"Yes, it would seem our leader wishes to end this quickly." Silas calmly responds with his arms crossed. "Very well, leave no one standing."

"Yes Sir!" The footsoldier teleports away as Silas continues to look over the fight (Zoras fighting off the Yiga, Zelda using her magic against the monsters and Samus fighting the corrupted Hinox).

"I still owe you for that night in the rain, my dear…" Silas eyes radiate with phazon energy as he stares at Samus from afar.

Samus continues her fight against the Hinox with slow progress, all the while distracted by the bombardment. "Virginia, who or what is firing at us?"

"Unknown, the storm clouds are interfering with the scanners."

Before Samus can retort, the Hinox punches her against a pillar on the bridge. Samus gets back on her feet and notices the Hinox charging at her. Samus smirks and charges her power beam and, with the Hinox in close proximity, jumps up and uppercuts it in the face with her charged cannon, knocking it back and holding its eye in discomfort. While it's down, Samus equips her nova beam (high frequency blasts) and activates her x-ray visor, which allows her to see the Hinox's phazon infused heart and with the nova beams piercing effects, blasts a hole through its chest and out its back, obliterating the heart. The now dead Hinox falls off the bridge and onto the shallow edge of the lake. Samus catches her breath and as she turns around, Silas stands before her.

"Hello Samus." Silas threateningly greets her.

"Out of my way; I have no time for you." Samus demands.

"Unfortunately, that's not how this works; if you want other opponents, you'll have to defeat me first."

"Fine then." Samus shoots a charged plasma beam shot at Silas and, to her shock, he catches it with his phazon powered right arm and with a clench of his hand, he disperses it.

"You'll have to do much better than that." Silas smiles maliciously.

* * *

The Zoras continue their struggle against the phazon powered Yiga and monsters, as well as the unknown attacker's bombardment. Leading the attack are Zelda and Sidon, who decided not to stray from one another.

"This never ends!" Sidon shouts in frustration while fighting off several monsters.

"We can do this! Just hold on!" Zelda replies before ducking down as a fireball flies above her and hits the canyon wall. "What is that thing?!"

"It has to be some form of guardian skywatcher! But this rain is making it hard to see anything in the sky!" One of the zora guards speaks up near her while wrestling with a Yiga footsoldier, doing everything he can to keep him away from Zelda and Sidon.

Zelda looks up to the sky and tries to identify the stranger, noticing at least that they have an almost avian appearance. "No, this is something else…" The stranger dive-bombs and delivers a payload of fireballs, catching several zoras off guard as they fall into the lake, much to the exhilaration of the Yiga. Frustrated, Zelda walks to the edge of the cliff, ignoring Sidon and the soldiers protests, and takes aim at the strangers silhouette as it turns back to fire once again. "This ends now!" Zelda lets loose her arrow, anticipating the strangers trajectory (taught to her by Urbosa back in the day), until…. ***CLANK!*** to her shock, the arrow bounces off of the stranger and even more unsettling, he appears to be made out of metal. Zelda and the others notice that the stranger stopped his bombardment and hovers just out of visibility.

"Was that you're best shot?" The stranger mockingly quips. "Well then, here's mine!" The declaration is followed by a stream of superheated energy, knocking Zelda off the edge of the cliff and towards the lake below the domain. "Now then- what?!" The stranger looks down where Zelda fell and sees a fireball hurtling towards him and impacts his chest.

"Got you…" Zelda weakly says before finally reaching the lake. The stranger screeches as he too falls out of the sky and into the lake. The Yiga shout in anger as the Zoras cheer.

"We need to recover the princess!" Sidon shouts as he removes the trident from the corpse of a Yiga blademaster. "Wait, where is Samus?"

* * *

Back on the bridge, Samus continues her fight against Silas, having switched back to her power suit (yellow suit with less detail and orange-yellow flat shoulders) due to the varia suit receiving too much damage.

"Are you giving up?" Silas mocks Samus while flexing his arm. "We were just getting started."

Ignoring him, Samus locks on to Silas and fires a missile, which he dodges and smirks at Samus. To his confusion, Samus smirks as well and then he is hit from behind by the same missile, having been given a guided feature from the lock-on.

"I'm not through yet." Samus states as she waits for the dust to clear. To her horror, Silas survived the blast by turning his right arm into a shield like appendage.

"Almost got me." Silas says. "I nearly forgot that your missiles can do that."

"How do you know that?" Samus asks, having never used missiles on him. "And how do you know what they're called?"

"Wouldn't you like to know?" Silas immediately closes the distance between them and turns his arm into a battering ram, which in turn smacks her against a pillar on the bridge. Samus tries to fire a shot, but Silas swats her cannon to the side and punches her square on the helmet, cracking her visor. "This is for being such a nuisance!" Silas grabs her by the helmet and, turning his arm into a piston like appendage, hits her in the chest/abdomen many times, whittling her armor away and causing her injury.

"Suit integrity critical! Contusions detected!" Virginia alerts, causing Samus to grab the piston with her left hand and repulses him with the booster on her heel. Breathing heavily, Samus drops to one knee and coughs, tasting blood as she does so. Silas lunges forward and in response, Samus intercepts him and bashes his head with her cannon. Silas backs off and checks the wound on his forehead.

"Heh, you got me." Silas then reverts his arm to normal and points it forward. "But, how will you deal with this?" A stream of phazon fires from his palm and Samus answers it with stream of energy from her cannon. Unfortunately, due to being previously weakened by Silas, her cannon is overtaken and damaged by the phazon, as well as her suit being damaged further.

"I have to say, Samus; you were a disappointment." Silas states, having stopped his attack. "You looked like a formidable fighter, but it was just a ruse." Samus looks up to meet his eyes, bits of her suit chipping off. "He was right all along; beneath the armor, weaponry and list of successes, you're just a little girl shouting for mommy and daddy." Samus stares at Silas in rage, transferring parts of her suit to restore her cannon. "How does that make you feel, _Sammy?_ " Silas cruelly chuckles, content that he humiliated Samus.

Infuriated, Samus uses the boosters on her back to lunge at Silas, landing three punches on his face, roundhouse kicking him in the chest and finishes with a plasma beam blast in the abdomen. She then picks him up by the collar and prepares to blast his head off.

Coughing up blood, Silas laughs at her rage. "Huh, I struck a nerve, didn't I? I'll make sure to be more sensitive next time. Heheh."

"You. Don't. Know me." Samus angrily responds as she moves her cannon closer to his head.

"I don't need to know, our friend knows plenty about you already. In fact, he's down there with the princess as we speak."

Alarmed, Samus turns her head to look below the bridge, giving Silas ample time to morph his arm into a blade and run it into her cannon and getting her arm in the process, causing Samus to shout in pain. He then kicks upward, destroying her already brittle helmet and then destroying several parts of her suit (left arm, right shoulder, abdomen, right thigh and left shin). Parrying one of his hits with her damaged cannon, Samus then pulls off the sickle from Silas belt and tries to slash at him, only for him to grab her arm and impale her through the abdomen with his blade arm. Struggling from the shock brought on by blood loss, Samus's sight begins to blur.

"* **cough*** I'll...kill you…"

"Oh, you tried; and you (brings the blade further in, causing Samus's eyes to widen, as well as exclaiming in pain) failed." Silas smiles sadistically. "You didn't think any one of you could stop us, did you?"

"Samus, yo-r v-als are cri-t-l. Seek me-c-l aid imm-iat-ly." Virginia attempts to report, but cannot form coherent words due to the immense damage to the suit.

"A shame that you came all this way, just to die. But, I suppose you can hear exactly how I know so much about you. Not like it matters now." Silas brings a quickly fading Samus close and whispers in her ear. "An old face from K2-L."

Samus's eyes widen briefly, unwilling to believe this revelation. Before anything else, Silas callously removes his blade from her abdomen and, unable to handle the injury, Samus falls to the ground unconscious.

"One down, two to go." Silas walks past Samus and motions towards the domain.

* * *

 **Meanwhile (A/N: everything up to this point happens at the same time), Zelda is brought up from the water by King Dorephan, who had taken it upon himself to save her from drowning.**

"Come now princess, breathe." King Dorephan cradles Zelda in his right arm; eventually she coughs out water and hastens to breathe. "Easy now, I've got you."

"King Dorephan? What are- *gasp*" Before she says anything else, Zelda notices the many cuts and bruises littering his body. "You're hurt!"

"Oh, this? It is nothing to get upset about. I've been through much worse than this. You are more important than a few scratches here and there."

"Because I'm the princess of Hyrule?" Zelda asks in a regretful tone.

"Partly. Mainly because of my dear Mipha." King Dorephan quietly states, much to Zelda's confusion. "While she loved Link deeply, you also meant a great deal to her. She appreciated you for your kindness and indomitable will and even hoped that, once she became a champion, you two could become friends. I will never allow any harm to befall you."

"We were friends, King Dorephan. Then and always." Zelda smiles while wiping away a few tears. "Thank you."

King Dorephan grins widely at her before looking up. "Now, we should return; our fight is not yet over. Can you still raise a sword, child?"

"I'm raring to go. Let's save your home; Mipha's home."

King Dorephan motions to climb up the wall to reach the domain, but a fireball knocks him off and he falls on his back, shielding Zelda from rubble with his arms.

"What was that?!" King Dorephan shouts as he looks to the water where the blast came from.

"There's something down there…" Zelda comments while squinting her eyes to focus….until finally noticing a pair of red eyes staring at them.

"Princess!" King Dorephan brings her close to shield her as the stranger erupts from the water and slams him against the wall and roars. King Dorephan recomposes himself and checks to see if Zelda is unharmed, who confirms him. They then finally see the strangers appearance: an avian/reptilian like creature with clawed bird like feet, clawed three fingered arms, a long tail ending in a spike, golden bat like wings, a pterodactyl like head with sharp teeth and piercing red eyes and metallic armor skin.

"What are you?" Zelda asks in fear.

"Heheheh….call me Ridley."

* * *

 **Inside the barrier, Link fights a losing battle against Dark Samus, having lost several parts of his suit and exposing his champion's tunic.**

"This is the best you can do…?" Dark Samus comments while walking towards Link. "To think that you were the one who awakened me after almost a century…"

"Had I known you were festering while Calamity Ganon grew in strength, I would have stopped you before things got out of hand." Link breathlessly says, using the master sword as a makeshift support.

"It no longer matters… You and your collaborators will die…" Dark Samus looks outside for a few seconds and then turns back. "Speaking of which…" She moves aside to allow Link to see a terrible sight; Samus on the ground and Silas standing over her.

"Samus!" Link tries to run over to help, despite his injuries, but is grabbed by Dark Samus.

"There is no escape from me…"

"Let go!" Link pulls out a phazon arrow from his quiver and jams it into her abdomen, causing her to scream and release her grip. Taking advantage of her brief vulnerability, Link follows up with a flurry rush of slashes, ending in a thrust to her chest. To his dismay, her vulnerability subsided quickly and the sword inflicted no damage, as well as recovering the wounds previously inflicted.

"Useless…" Dark Samus punches him in the stomach, winding him, and follows up with a force field that throws him backwards. She then teleports behind him and kicks Link in the back, making him fall to the ground. "Stop me then…? You can't even defeat me now…" Dark Samus notices that the fighting outside has stopped and communicates to Ridley. "It is time…"

* * *

Despite his best efforts, King Dorephan stood no chance against Ridley and lies defeated.

"King Dorephan! You must get up!" Zelda shouts in despair as she kneels down to speak to him.

"Princess… Run…" King Dorephan weakly says before fainting.

"Hahahah… That was the most he could come up with? How have these fools not taken over yet?" Ridley mocks, referring to the Yiga. "Now, I believe we have some unfinished business, you and I."

Ridley flies forward and grabs Zelda as she unsuccessfully prepares Din's Fire. Before he can do anything else, he receives a telepathic message from Dark Samus.

"Aww, over already? Very well then." Ridley looks down at Zelda, still clutched in his hand. "We'll come back to this later. For now, we have a little surprise for you and your friends." Ridley flies up and Zelda shouts in horror at seeing Samus face down on the bridge. "Another shame; _I_ wanted to destroy her."

Ridley drops Zelda from a short height into the domain and sees the surviving Zoras on their knees with their hands behind their heads with the Yiga patrolling them before perching himself on the cliffs overlooking the domain.

"So, here we are; with you people at our mercy." Silas comments while stepping over a fallen Zora soldier. "You've put up quite the valiant resistance; misguided, but valiant." As he says this, the barrier lowers. "Ah, the fight is over, it seems."

Once fully lowered, Zelda stares in horror as Dark Samus walks out with Link being dragged from her left hand while the Yiga cheer.

"This is your champion…?" Dark Samus brings him up so everyone present can see Link, defeated. "Your leader…? Your savior…?" She then tosses him in front of Zelda. "No… I am."

The Yiga erupt in thunderous applause over their apparent victory as Zelda reaches over to Link, sadly acknowledging their defeat.

"This victory is yours, my liege. Even with the fall of Vah Ruta, the rest of the land is still under our control." Silas comments, showing everyone present the massive barrier still covering the other regions. "Face the truth, all ye foolish enough to challenge her; you have lost." Zelda and the Zoras lower their heads in shame as he says this. 'Let this be a lesson to all would-be resistance; that idea is very dangerous. All races, Hylian or otherwise, are insignificant creatures, put on this world to serve our conquest!" The other Yiga grunt in approval at Silas words.

"You're wrong, Silas." Sidon speaks up as everyone faces him. "We are not here to serve you or that monster." Silas slowly walks over to Sidon, finding amusement in his bravado. "I don't see the Yiga here, just a gaggle of slaves who think that their _leader_ only wants them to reach greatness! So, who is the insignificant one here? We will not bow to you! Just like Ganon, you will fail!" The Zoras and Zelda look up and find inspiration in Sidon's words; Link even begins to regain consciousness. Before Silas can retort Dark Samus teleports in front of Sidon and seizes him by the throat and forms a phazon blade below her cannon (similar to a bayonet).

"Very well...You die first…" Dark Samus prepares to impale Sidon, who shows no fear, in the chest before being blocked by Link, who then forces her back into the center of the domain. A few of the Yiga attempt to aid her, but Silas stops them, telling them to "Let the champion have his fun".

Zelda gets up and runs to help Link, only to be restrained by Silas. "No no, you're staying with me, _your highness._ We wouldn't want you to miss even a second of this." Silas notices that Zelda is trying to summon her power, but he quickly shuts that idea down. "One spell and we start killing hostages, do you understand?" Zelda shoots him an icy glare, but concedes and dispels her magic. "That's better."

Link forces Dark Samus to the center, repels her and slashes across her chest, which quickly regenerates. Undeterred, he thrusts the sword and Dark Samus parries it, following up with a shot which Link deflects back at her (with his shield), leaving her briefly vulnerable to further attack. Taking advantage of this, Link lands a brutal downward strike on her chest, causing Dark Samus to yell, and he follows up by stabbing a phazon arrow on her left temple. She backs off, pulls out the arrow in discomfort, glares angrily at Link and cartwheels to the left as another replica of her cartwheels to the right from her. "I have plenty more…" Dark Samus orders her Echo to attack while she fires several phazon shots in the air, which begin to home in on Link. He dodges the shots and blocks the phazon stream from the Dark Echo, but is forced to roll away as Dark Samus appears behind him and fires another stream. The Echo morphs into a ball and slams into Link, making him fall to the ground and giving Dark Samus the chance to jump up and slam down on him. To counter her attack, Link conjures Revali's Gale to propel him upward and punches her in the visor. As they both fall back down, Link slams the master sword down on the unsuspecting Echo, destroying it. Searching for Dark Samus, he notices her floating above him with two more Echoes in a triangle formation before firing a large burst of phazon each. Link quickly conjures Daruk's Protection, which then redirects the blasts, destroying the Echoes and injuring Dark Samus significantly.

"That's it Link! You've got this!" Sidon shouts his praise as another Yiga tries to keep him quiet. This proves to be mostly unsuccessful as Zelda and the Zoras begin to lose their apprehension and gain confidence. Recomposing herself, Dark Samus fires a salvo of missiles at Link, which he manages to dodge by rolling to the side. This proved to be merely a distraction, as she takes advantage of his move by teleporting next to him and then kicking him to the side then following up with a boost ball to his chest before Link can react. Dark Samus flies up and prepares to slam down on Link, who brings up the master sword and holds it horizontally. She impacts her charged cannon on the blade and in response; it glows with a white light. The sword dispels the blast and has Dark Samus land a few inches away. "What is this…?" Link stands up as everyone else stares in awe at the splendor of the master swords white light and, unbeknownst to everyone else, Samus begins to regain consciousness.

"You're no savior." Link declares as he menacingly points the sword at Dark Samus. "You are nothing but a plague upon this world and we will stop you!" Link charges forward and before she can react, he slashes Dark Samus across the abdomen. To her shock, the blade managed to cause her damage.

"My liege!" Silas screams in fury, giving Zelda the opportunity to elbow him in the stomach and use her power to repel him away. The Yiga glare at Zelda, but their distraction proves to be their undoing as the Zoras rise up and fight them off. Ridley, witnessing these events, dive-bombs the domain but is struck down by a large boulder, which was thrown by King Dorephan (still injured). Sidon goes over to Zelda as they are approached by a Yiga footsoldier and before he can attack, he is hit by 5 shots from Samus's (still on the ground) pistol, sending him plummeting over the side.

"Samus!" Zelda shouts in a mix of joy and concern over Samus's condition. "Are you alright?!"

"I've seen better days…" Samus weakly quips.

"Don't move, we're coming to get you." Sidon declares as he and Zelda move to aid Samus.

Back to the main conflict, Link continues to overpower Dark Samus, leaving several lacerations on her. Realizing that his fatigue from fighting the queen metroid and his earlier fight with Dark Samus is beginning to catch up to him, Link moves in to finish the fight. She fires a stream of phazon as Link throws the master sword, splitting the stream and then impaling Dark Samus through her left pectoral. As she falls to her knees, Link moves in and brutally removes the sword upward and Dark Samus falls to the ground. Link breathes heavily as the sword loses its glow. "It's finished." Link turns around and sees that both sides have stopped fighting and are now staring at him. The silence is broken as the Yiga begin to cheer, much to everyone else's confusion.

"Have they gone insane?" Link wonders aloud before seeing Zelda, Sidon (with Samus on his back) and the Zoras staring in horror at the scene behind him; Link turns around to see Dark Samus floating in the air, absorbing phazon to fully restore her body and powering her even further. "This can't be!" Link shouts in disbelief.

"You don't understand, do you…?" Dark Samus slowly floats back to the ground. "The phazon gives me power… As long as it exists, I am invincible…"

Frustrated, Link charges with the sword drawn (Zelda shouting in vain to stop him), this proves to be futile as Dark Samus knees him in the stomach, bashes him on the head with her cannon and blasts him away (the Yiga cheer as the other watch in despair).

"Link!" Zelda shouts in terror, only being held back by Sidon. "She's killing him! Let go of me!"

"You were right, young hero…." Dark Samus grabs Link (battered and bloodied) by the collar, who only stares in defiance. "It ends now…" She then blasts him with a burst of phazon to his chest, causing him to fly towards a wall that breaks from the sheer force of the impact; the dust clears and Link is seen lying face down on the ground. The Yiga erupt in applause, chanting her name and holding their weapons high, while the zoras drop their heads in defeat (Zelda, in particular, looking on with tears running down her cheeks).

"Now, there will be no more interruptions, I assume…?" Dark Samus then looks to the side and sees the master sword sticking out of the ground and approaches it. "I claim your sword as the spoils of war…" She grabs it by the handle and, in a matter of seconds, is seized by excruciating pain while the master sword glows in a bright, golden light. She releases the sword and drops to her knees as the Yiga abandon the zoras and head to aid their master. Dark Samus then hears a voice in her head, which can only be described as divine; "Abomination, this sacred blade was never meant for you." She then makes the shocking discovery that the master sword significantly weakened her ability to absorb phazon and even left her near death.

"My liege!" Silas shouts in worry as he approaches her. "Fear not, we have you." He turns around and sees the zoras with their weapons ready, Sidon with his trident and a serious expression, King Dorephan pointing his silver longsword at the Yiga and Zelda with her flaming hands ready.

"Men, we must retreat…" Silas quietly announces. "Leave, now. Take our master away from here." The remaining Yiga teleport away with Dark Samus, only Silas stays behind. "This is the only time you will ever see us retreat." Silas points at the zoras with his phazon arm while glaring. "Next time, we will leave with the satisfaction of having ended your lives. Enjoy what little time you have left." Silas finally teleports away, while from behind the zoras, Ridley jumps up in the air and flies away while roaring in anger. With the threat averted, the zoras tend to Samus's injuries (who had fallen unconscious once again), the injured zoras are looked after by the healers and both Zelda and Sidon rush towards Link.

"Link, can you hear me?" Sidon asks in worry after placing Link on his back. Link then opens his eyes slightly.

"You'll be alright, Link. We've driven them off." Zelda says as she places her hands on his cheeks. Link smiles slightly as his consciousness begins to fade, everyone else gathering around him being the last thing he sees. "Just hold on, Link. Hold on…" Zeldas words echo as Link finally passes out.

* * *

 **Ten hours later.**

Link slowly awakens to the sound of falling rain in a house he doesn't immediately recognize. He sits up from the bed, groaning from his injuries (most of which have healed), and finally recognizes the house; Impa's residence.

"I'm in Kakariko Village? How?" Link wonders aloud before looking down to see that his champion's tunic was removed and replaced with a simple white shirt, as well as his suit (or what remained of it) missing. Before he can ponder it further, he becomes distracted by the sound of footsteps coming from the stairs.

"Master Link!" Paya beams at seeing Link and kneels beside him. "Are you alright? Do you need anything?"

"Hello Paya. No thanks, but how did I get here?"

"W-well, when you didn't come back after dispelling the barrier, Grandmother sent Dorian and Cado to find out what was keeping you."

"What about the others? Are they- ugh." Link tries to get up, but his bruises affect him. Paya then stops him by placing her hands on his shoulders.

"T-they're fine." Paya answers, blushing slightly from the brief contact. "Princess Zelda and Prince Sidon are alright, b-but you and Miss Samus were terribly injured, we brought you here to heal. I was so s-scared…"

Link grabs her hand and gives her a reassuring smile. "Thanks for looking out for me. I'll be fine now." Paya, still with flushed cheeks, smiles back in response. "Can you take me to the others now? I want to know how they are."

"Yes Master Link, right away." Link puts his boots on and Paya helps him on his feet. They both make for the stairs with Paya supporting Link.

"By the way, where's my tunic? Who has it?"

"Aahh!" Paya's face turns into a deep shade of red at Link's question. "W-why would I kn-know about that?! I didn't r-remove it from you w-while you were s-sleeping, if that is w-what you're insinuating! I just w-watched you sleep peacefully- ahh! That isn't what it sounds like!"

"It's ok." Link puts up his left hand to slow her down. "I'm sure that Impa has it, right?"

"Oh, yes. That was obvious, wasn't it?" Paya answers while lowering her head in embarrassment. The pair reaches the first floor, where they are greeted by Zelda, Samus, Impa and Sidon.

"Link! Thank goodness!" Zelda gleefully embraces Link, much to his discomfort. "Does anything still hurt?"

"Not at first, but I feel something now, ouch." Link answers while wincing, but returns the hug regardless. He then turns to Samus, who is wearing a grey robe and slippers and with several bandages and her hair down. "Samus, are you alright?"

"I've looked worse, believe me." Samus answers with a slightly displeased tone.

"How are you back on your feet so quickly?"

"Thanks to my Chozo physiology, wounds tend to heal much more quickly." Samus then looks at Paya. "Thank you for tending to me, Paya."

"Anything for a friend." Paya answers while smiling.

"I'm thankful that everyone is, for the most part, recovered. But, I believe that we have much to discuss." Impa speaks up from her seat. Agreeing, everyone sits down on their mats and they bring Impa up to speed with what they encountered in Lanayru. "I see. Then this phazon is even more dangerous than previously established."

"Yes, but it no longer plagues Lanayru, Hateno or Dueling Peaks." Sidon adds, hoping to lift their spirits.

"While that is a victory, the barrier still covers the rest of the land." Impa speaks up. "I fear our troubles are far from over."

"I agree; this corruption won't stop until all of the phazon is purged." Samus retorts with conviction. "And we won't stop either."

"This is our home; we will never give it up." Zelda joins Samus in her conviction.

"No doppelganger is going to rule over this land, believe me." Sidon flexes his arm.

"I will not give in until that Leviathan is destroyed." Link stands up and declares with resolve, the master sword glowing behind him in a small shrine that was put together to house it.

Knowing how important their mission is, the group resolves to never waver and to keep fighting, for many people's lives rest on their shoulders.

The battle has only just begun.

* * *

Meanwhile, in the new Yiga clan hideout, Silas observes Dark Samus in a peculiar pod. The brief contact with the Master Sword's hilt has severely weakened her to the point of death, restricting her to the pod to rejuvenate.

"Rest and heal, my liege. Your faithful servants will continue your noble work while you recover." Silas then walks away while Ridley looks on from his perch within the chamber. "It is only a matter of time; we will not stop until this world is purified."

From inside the chamber, Dark Samus weakly flexes her left hand and her visor glows slightly.

 **To be continued.**

* * *

 **Authors note: Well, yet another long chapter. I know I'm probably going to get a lot of hate for how badly Link and Samus were beaten in this chapter, but I decided to go with it because there is something that we kind of have to remember; heroes are not invincible, but they can still overcome the obstacle even after losing at first. In case some of you haven't figured it out, that wasn't Fi that spoke to Dark Samus when she tried to grab the sword; it was actually Hylia. So, that was the end of part one I guess, but don't get nuts; I'm not going on hiatus, I just see significant events as** _ **parts**_ **. With that in mind, I think I should give you guys some hints as to what you'll see in "Part Two" (aka the next chapters):**

 **Dragons**

 **Lurelin Village**

 **Eventide Island**

 **Space Pirate**

 **Project Helix**

 **Eldin Region**

 **Exposure….**

 **K2-L**

 **And that's about all I can give for now. See you soon!**


	11. Chapter 11 Mystery at Eventide Island

**Chapter 11: Mystery at Eventide Island**

" _The less you reveal, the more people can wonder"_

 **Data log entry SA38416.20X6: My ships onboard computer recognized an energy signature originating from a distant planet far away from Galactic Federation jurisdiction. This energy was proven to be phazon, thought destroyed long ago in the eradication of the planet Phaaze (source of all phazon in the galaxy), yet it has appeared on this planet, spreading the corruption and bringing the threat back to the galaxy. Original Intel suggests that the source is from a surviving Leviathan seed, which impacted the land almost a century ago and has festered over that time. Even more unsettling is the reappearance of Dark Samus, who has managed to corrupt the minds of a group of insurgents known on this planet as the Yiga and spreads the phazon strategically over several regions through what appear to be ancient machines native to the land. One of the results of the corruption came in the form of metroids, once believed to be extinct. Surprisingly, they were able to metamorph into their other stages without the aid of aeion (energy native to their former home world: SR388), my only conclusion is that they were able to achieve this by feeding on the living creatures here and the already chaotic nature of the phazon. Thankfully, we managed to eliminate the metroid threat once again with the aid of Link (A young soldier with the disposition of a seasoned war veteran and surprisingly impressive reflexes and swordsmanship skill) and Zelda (Princess of this land and, supposedly, the last living member of the royal family. On another note, she has abilities that make her more of a sorceress than a princess, more information is needed to make a final assessment on her power). Now, the next step is to find all the sources that generate the barrier over the land. Samus Aran, signing out.**

 **Additional reports**

 **Link: A young swordsman and knight of Hyrule. Possessing uncanny reflexes and masterful sword techniques, Link was hailed over a century ago as the chosen hero of the goddess. Now seen as the last champion of the previous generation, he takes his role as the princess's knight very seriously.**

 **Zelda: Princess of Hyrule and last living member of the royal family. Her small frame hides an enormous power that allows her to perform unimaginable feats. Although headstrong and magnanimous, her status as the heir to the throne makes her a prime target for the Yiga.**

 **Sidon: Crown prince and new champion of the Zoras. A close friend of Link, Sidon shows all the qualities to not only be a protector, but also a great king; willpower, strength, loyalty and a strong sense of duty. As the new champion, he is charged with piloting divine beast Vah Ruta.**

 **Silas: The current leader of the Yiga and second-in-command of the corrupted forces. A virtually aggressive man, Silas employs a phazon powered right arm to replace the one previously shot off. He claims that he and the others follow Dark Samus out of loyalty, but it is clear that their minds have been altered just like others before them. One thing is certain though; he harbors an intense grudge against me and the feeling is becoming mutual.**

 **Dark Samus: The ruler of the corrupted and mastermind behind the spread of the phazon in this world. Originally known as Metroid Prime, she has been reborn into a new form resembling my own suit (taken from the Phazon Suit, specifically). Her affinity with phazon has made her significantly stronger as she is able to absorb vast amounts of it and channel them into destructive blasts among other things. Cold, calculating and utterly merciless, Dark Samus will wipe out all who stand in her path of conquest.**

* * *

Samus powers down her ships logbook and then exits it. The trio had spent the whole day recovering and strengthening themselves from their encounter with Dark Samus and the Yiga. Link, having fully healed from his injuries, swings a torch in different directions. Zelda, standing next to him, uses another torch to copy his movements, having taken up Link's offer to learn more sword techniques. Samus observes this and her mind wanders back to the small conversation she had with Zelda.

* * *

Three hours after arriving back to the village from the domain, Samus awakens in a bed wearing a robe and her wound stitched up. Wearily, she gets up and sees Link sleeping in the bed across from her and, not wanting to wake him up, she quietly walks downstairs. Upon reaching the first floor, she sees the master sword in a small alter and remembering what happened to Dark Samus, she decides to approach it. Seeing that her bracelet was the only thing left on her after the suit was removed, Samus brings it up to face the sword.

"Virginia, give me a scan of the swords composition."

"Scanning…" A small light strokes the sword from blade to hilt. "Unknown; the swords composition doesn't match any element on any known periodic table. The metal doesn't seem to even exist." Virginia gives her report to a confused Samus.

"It doesn't match anything and its metal resembles stainless steel which isn't actually steel; _what is this thing_?" Samus reaches out to grab the hilt, but is stopped by Zelda, who came in through the front door.

"No, you must not touch this sword." Zelda calmly says while moving Samus's hand away.

"Zelda, what exactly is this sword?" Samus asks.

"I'll give you the brief version; this is the Master Sword, also known as the Blade of Evil's Bane. Only the chosen hero or the royal family can wield it."

"But, who forged it? Using what materials?"

"It was created by the goddess Hylia, forged from her powers and those of the three golden goddesses; Din, Nayru and Farore. I assume you know already what happens if anyone other than the ones I previously mentioned touch the sword?"

"It harms them. Badly."

"Yes. Had Dark Samus held on any longer, it might have even been enough to kill her."

"If only we could be so lucky." Samus comments with a low tone.

"But, enough of this history lesson." Zelda smiles as she looks at Samus. "How are you? Are you feeling better?"

"I'm getting there. You did a fine job with the stitches, thank you." Samus gives her a reassuring smile.

"Oh, that wasn't me; it was Paya. She tended to both you and Link's wounds. Speaking of which, has he woken up yet?"

"Not yet, he took a serious beating after all. But, he should be up later, given his willpower. Also, remind me to thank Paya later."

"You may see her now; Dorian's daughter made supper for us, you should come and have some. We should leave some for Link or we will never hear the end of it." Zelda quips while offering the way outside. Samus nods and follows her out, not before taking one final glance at the Master Sword.

* * *

"Samus, the suits have been repaired. I have also taken the liberty of strengthening their overall durability." Virginia reports, snapping Samus out of her thoughts.

"Copied. Thank you, Virginia." Samus then notices Link and Zelda walking towards her.

"Are you ok? You were just staring off into space." Link asks with curiosity.

"Are you feeling sick? We can offer you some potions." Zelda generously offers.

"No, I'm fine. Thanks." Samus brings up her hands to dismiss their concerns. "I just wanted to say that the suits have been fixed. If you're both ready, we can continue on to other areas now."

"Yes, of course; we should go immediately." Zelda speaks up.

"I'm ready when you are." Link says while rubbing his left shoulder. "But, where should we start?"

"Forgive the interruption, but there is a matter that needs to be addressed." Virginia comments, causing all three of them to pay attention. "Due to the partial removal of the barrier, my scanners have been expanded. I detected Space Pirate technology in the southeastern portion of the continent." Virginia brings up a map of Hyrule and pinpoints an island off of southeastern coast.

"Hey, that's Eventide Island." Link says with surprise.

"You know where this is?" Samus asks.

"Yeah, it's a solitary island that has a shrine on it. Aside from that, there's not much to it."

"I think we should pay this island a visit, we may have some uninvited guests there." Samus says with a serious tone.

* * *

The three ready themselves and begin preparations to take off. Before leaving, Impa stops them briefly.

"Well, it looks like you've ended your respite. Must you really leave now?"

"I'm afraid so. The longer we wait, the more phazon spreads across the land." Zelda apologetically says. "Besides, we have something to investigate."

"Hmm, well don't let us keep you. Just be very careful, the Yiga have become much more ruthless; their defeat in Lanayru will not bode well with them and they will most certainly seek vengeance."

"Let them try, I'll show them that we're not as weak as they think." Link says with determination.

"Careful, don't let hubris be your undoing." Impa offers some wisdom. "Stay level headed and keep your wits about you." The three nod in acknowledgement. "Ooh, did it get colder?"

"Huh, now that you mention it, it does feel cold." Zelda confirms while rubbing her hands.

"Grandmother, what's going on? Why did it get so cold all of a sudden?" Paya walks up and wonders aloud.

"That's odd; it's too early in the year to be this cold." Link comments.

"What's causing this massive drop in the temperature?" Samus wonders, Virginia being unable confirm anything.

"What's this?" Sidon, from another part of the village, notices a cold fog beginning to appear, earning surprise from the villagers. "Link, where are you?"

"Sidon? Just stay where you are, this is no ordinary fog!" Link shouts in alarm.

Soon the fog becomes so thick that nothing can be seen. The panicked villagers scramble to find their families until they all stop to hear low growling from an unspecified location. Zelda tries to see through the fog, until a large eye (yellow and blue iris with a pinkish cornea) opens up in front of her. Startled, she reels back as Link and Samus come to her aid. The fog dissipates and we see what the eye belongs to; a massive, white serpentine dragon with long ears, a purple underbelly, three pairs of clawed feet (two pairs up front and one pair of hind legs), a great mane composed of large icicles and icy spines that run down its back ending in large spikes on its tail.

"I don't believe it; the great dragon Naydra!" Impa says in astonishment while everyone else watches in a mix of fear and amazement.

" _Who dares to defile my mistresses' sacred blade? Who dares to bring misery to this land?"_ Naydra proclaims in a loud, booming voice.

"What did it say?" Samus asks, unable to understand Naydra's language.

"I cannot decipher the language; it isn't the same that all others here speak." Virginia states.

"Great, now what?" Link asks as Zelda pats his shoulder.

"Don't worry, I'll handle this." Zelda walks up to Naydra, ignoring everyone else's protests. Naydra notices this and lowers his head to be at eye level with Zelda.

" _Who are you, little one?"_

" _Great dragon Naydra, I am Zelda, princess of Hyrule."_ Zelda answers the dragon in the same language, much to everyone's shock. _"Forgive the others for not answering you, this language has been long forgotten by many."_

" _So, you are the one who holds the blood of my mistress. It pleases me greatly to know that her spirit carries on. You must know then; who tried to take the Master Sword?"_

" _A scourge from another world has come to claim ours; they tried to take the sword but were unable to do so. The chosen hero still stands tall, the Master sword remains his."_

Zelda continues to explain the situation in further detail (Samus, the Yiga, the phazon, the metroids, Dark Samus, etc.). At the end of her testimony, Naydra speaks up.

" _Princess Zelda, I thank you for telling me of this world's peril. Know that, as the reincarnation of the goddess, we are at your beck and call when you need us."_

" _Thank you, great dragon Naydra."_ Zelda gracefully curtsies.

Naydra then looks at Link, who bows in respect to the dragon. _"I remember you, from the Spring of Wisdom. You freed me from Ganon's malice."_ Naydra comments before lowering his head in acknowledgement.

Naydra now focuses his attention on Samus. To her surprise, he exhales a puff of snow at her. _"May the goddess smile upon you."_

Naydra gives a proud roar before ascending to the sky and opening a rift into another dimension, which he enters. The rift closes behind him and the temperature regulates itself.

"He likes you." Zelda giggles at Samus, who wipes the snow off of her visor.

"My girl, I had no idea you spoke ancient Hylian." Impa says with surprise.

"I studied it when I had free time back then. I think it's wise to know it and not need it, than not know it at all."

"I honestly can't believe that dragons exist, let alone ones that talk." Samus comments. "Well, given the other things I've seen before, it shouldn't be too surprising."

"He's one of three dragons. We might see them on the way.' Link speaks up. "Now, I think we should head out. I want to know what's going on at Eventide Island."

As the three move towards the ship, Sidon approaches Link to give his parting words.

"I thank you all once more for helping to save my home. I wish you luck on your journey, you have the aid of the Zoras whenever you may need it." Sidon proclaims with conviction. "You need only call upon us."

"Thanks Sidon. Link smiles while offering his hand, which Sidon accepts. "I won't let you down."

"What will you do now?" Zelda asks.

"I will return to Zora's Domain. There is much work to be done there and I must not leave my people unguarded."

"Very well, I wish you a safe journey back home." Zelda answers and before they can finish boarding, Paya approaches them with a basket hanging from her hands.

"Wait! Before you go, take this with you. I had it filled with several potions and many other first aid materials; you might need them where you're going." Paya says with her head lowered, a sign of her shyness.

"That's very kind of you, thank you Paya." Zelda smiles and gratefully accepts the basket.

"Yes, and thanks again for tending to our wounds during our stay." Samus adds, causing Paya to quickly nod in response, earning a chuckle from Impa. With nothing more to say, the three board the ship and take off for Eventide Island with Impa, Sidon and Paya lingering to see the ship disappear from view.

* * *

Meanwhile, in an unknown area, Silas walks into a cave guarded by several Yiga and is approached by one of them and they converse while not stopping at all.

"Master Silas, is it time now?"

"Yes, I've managed to find plenty of it." Silas holds up a canister to show the guard. "There are others searching for more, it will come in handy later."

"Master Silas, is this a wise course of action? We may be creating something that we could lose control over."

"Nonsense. We need more fighters and doing this will give us very powerful combatants. Our liege will be most pleased when she sees what we will bring her. Now, how long will it take for them to change?"

"Well, according to the texts we've found, a few hours in such an enclosed area will provoke the change. Nevertheless, they will look very different by the time you return."

"Good. We'll start with these." Silas and the guard reach a door (resembling more of a safe), which the latter opens. Upon entering, they are greeted by low growling and shrieks from within; groups of Bokoblins, Moblins, Lizalfos (muzzled) and Lynels (also muzzled) of all types reside in the large dungeon (illuminated by several torches), chained up. "Did you have any trouble catching them?"

"Our new powers made it easier; there are still other squads out looking for more." The guard answers directly.

"Excellent. Now, let's begin." Silas tosses the canister inside, breaking it, and the guard quickly shuts the door. The contents of the canister are revealed to be malice, which vapors of it circulate in the air of the dungeon. Silas and the guard walk back to the cave entrance, which several Yiga come in with bound, angry monsters with the intent of locking them up in several other dungeons. Other soldiers toss the monsters weapons onto an ever growing pile of them and a select few holding canisters of malice.

* * *

 **On the path to Eventide Island**

"Wow, you, Linky and Sammy went through a lot." Purah says to Zelda, from inside the Sheikah Slate. "No wonder the barrier is down from here at least."

"Yes, but it's still covering much of the land. If we've learned anything from the barrier, it's that the divine beasts are generating it." Zelda answers.

"Speaking of which, did you manage to connect to the towers?" Link cuts in.

"Yeah, I did. But without the other towers in the barrier, I can't see much of anything."

"So, we need to connect to every single tower in order to even attempt to find the seed. I knew it wouldn't be that easy." Samus laments.

"Regardless, we will keep you informed of any changes. For now, we have a lead on a possible intruder."

"Ok Zellie, I'll do what I can from here. Thankfully, Symin is working with Bolson's workers to get our guardians up and running for village defense, so there's that. Bye!" Purah does a pose before cutting off the connection. The remainder of the flight is left in silence while Link wonders to himself why Bolson, who is the man that runs the construction, wasn't mentioned and why he didn't see him when they visited Hateno.

* * *

 **Eventide Island**

The ship lands at the shores of the island and before they leave, the trio goes over their rules once again; don't wander too far from each other, keep their guard up and report anything suspicious. The three exit the ship and cautiously have their cannon and bows aimed. After around forty minutes of searching, Link calls out to the others to head to his position. "I think you better come see this." He points to a stretch of ground leading to the ocean, as if something was dragged.

"What happened here?" Zelda asks with curiosity.

"Was this here the last time you came?" Samus asks to Link while kneeling down, to which Link answers; "No, this is definitely new."

"Hmm, let's see if what ever did this is still down there." Samus scans the area near the site and picks up some large metallic object. "I see something, I think it's a ship. Question is; how do we get it up here?"

"I think I know." Link asks Zelda to hand him the Sheikah Slate and he activates the magnesis rune. With some difficulty, he manages to grab the submerged object and bring it up to the shore. The object in question is revealed to be a green, horseshoe crab shaped ship (two small wings jutting out from the sides, a tail like apparatus at the end and a bat-like symbol on the roof). "I take it this belongs to those space pirates?"

"That's it alright. Now, let's see what's inside." Samus activates the ship using her scan visor, the hatch opens and reveals that the pilot is missing.

"What? There's no one here." Zelda comments with surprise (taking pictures as well). "Where did they go?"

"I don't know, did they jump out at the last minute?" Link tries to find an answer.

"Pardon me, I've taken the liberty to scan the vessels interior and I managed to see that the ships skiff is missing." Virginia reports.

"So, the pilot did survive after all." Samus confirms. "Virginia, can you check when this ship crashed here?"

"According to the ships log, it arrived approximately two months ago."

The group was surprised by this announcement; a whole two months had passed since this ship arrived. Instead of answering one question, it left behind several; why did the space pirate come here? Why didn't it contact its comrades? How has no one seen or made mention of it within the two months? And most importantly, where did it go? If the trio had any hope of finding out some answers, it would be at the beachside settlement of Lurelin Village.

* * *

After leaving Eventide Island and activating the vessels self-destruct mechanism to prevent any future inconveniences, the group arrives at Lurelin Village. Upon seeing Link and Zelda step out, the now relaxed villagers greet them with open arms.

"Link! Good to see you again!" Rozel, an old man with shaggy white hair (complete with a beard and mustache), brown shoes, grey pants and a green jacket with a white undershirt as well as one of the many fishermen of the village, greets Link by patting his shoulders. "What brings you to our village? You finally come by for some R&R?"

"Hi Rozel, we're actually here on business. Though, when it's over, I may take that offer." Link answers with a friendly tone, indicating familiarity with the kind old man.

"And who's 'we'?" Rozel then looks behind Link to see Zelda, having completely forgotten that she was there. "Ah, Princess! Forgive my lack of manners, I overlooked you." Rozel straightens up and lowers his head in repentance. The other villagers follow his lead and bow in respect

"It's quite alright, sir. There's no need for dramatics with me, so please stop." Zelda responds quickly with her hands up and cheeks red at all of the unwanted attention, causing Samus to chuckle and further aggravate Zelda's discomfort.

"It's fine, Rozel. We just need to ask some questions and we'll be on our way." Link says, causing Rozel to hunch back down and rub his back in discomfort.

"Well, why didn't you just say so? Come on over to my house, my son just prepared supper. We can talk then." Agreeing, Link helps Rozel over to his house while Zelda (with her hands over her face) and Samus following behind. On the way, Rozel asks who the "bulky, orange guy" is, to which Link responds "a new friend."

* * *

 **Akkala Citadel**

Silas overlooks the entire region from the top of the citadel, until he is interrupted by another footsoldier holding a sword.

"Master Silas, we've received another shipment of weapons from Eldin. Our liege requested that this one be brought to you specifically, for your continued service."

"Ah, let me see it then." The footsoldier passes Silas the sword, which he unsheathes and sees a red windcleaver. "It's the rare variant, exquisite. Have we finished off the rest of them?"

"We're still scouring the region, but we've found one." The footsoldier signals to the others behind him and they bring in their prisoner; a Hylian soldier. They throw him at the center and Silas walks up to the soldier, who only gets on his knees and glares at him.

"Excellent work, little soldier; you've made it back to your outpost in one piece." Silas mockingly announces as the other Yiga present laugh in derision. "Now, maybe you can help us out; we're looking for the rest of your friends to _relieve them of duty._ Can you tell us where they are?"

"No." The soldier defiantly answers.

"No? May I ask why?"

"No soldier of Hyrule will ever betray their own. I'll take my knowledge to the grave."

"How noble. Pity that there won't be any Hyrule left when we conquer it all. So, I'll give you one more chance, because I enjoy your surplus of a spine; tell us where your compatriots are and we'll give you a swift end."

"Burn in whatever hell you and these unholy monsters crawled out of!" The soldier angrily shouts, causing the Yiga to mockingly applaud him.

"Heheheh, I like your attitude." Silas puts his new sword away and kneels down to be at eye level with the soldier. "You would have made a great addition to our ranks, it's a shame really." Silas extends his fingers into five sharp needles that impale the soldier through the chest and abdomen. The Yiga holler in triumph as the soldier convulses in agony. Silas removes his hand and lets him fall on the ground, convulsing as the blood seeps out from his wounds. Before anymore can be done, Dark Samus flies up and lands at the top, the Yiga kneel in response.

"My liege, you should be resting. You've not fully healed." Silas speaks with respect.

"I have enough strength for this…" Dark Samus coldly responds before looking at the dying soldier. "Have you finished off the remaining resistance…?"

"It's currently in progress, this one decided to die for his country and not tell us anything. I said he would've made a good addition to our ranks, yet he dies like a butchered animal."

Dark Samus looks at the soldier again and notices a little bit of life left in him. She then kneels down and drives her index finger into his chest. "You may get your wish yet, Silas…" The soldiers wounds instantly heal and his eyes open wide, revealing his irises have turned from brown to piercing blue, a sign of corruption. Dark Samus stands up and the now corrupted soldier gets on his feet.

"I am at your beck and call, my liege." The soldier declares.

"Go with the others; tell them all that you know…" Dark Samus orders, the soldier follows the other Yiga down the stairs and Silas stays behind to heed Dark Samus's orders. "Now, I want you to make sure that everything continues its current course at Eldin… Make sure the workers keep mining the crystals… The Elites are to be stationed at key points in the region, all resistance is to be snuffed out… Understood…?"

"Yes, my liege. All of those who dare will know pain." Silas declares with conviction.

"Good…" Dark Samus flies away and Silas walks down the stairs and continues his efforts to find the remaining soldiers.

* * *

Back at Lurelin Village, the group had finished their supper of pepper seafood and they explain everything that is going on.

"So, this blue wall that covers most of the land is because of some disease that changes everybody it touches? Well, good thing it never showed up here." Rozel comments.

"The barrier never covered this area?" Link asks with surprise.

"No, both Faron and the lake regions were uncovered." Numar, Rozel's son, answers.

"How fortunate. We should tell Purah about this later, she can connect to the towers here." Zelda optimistically says.

"Be wary, even though it hasn't shown up here, don't lose sight of any oddities that could appear." Samus (zero suit) warns. "Now, I think we should tell you the real reason we're here; have you seen anything like this?" Samus uses her helmet to project a holographic image of a space pirate (a creature with an angular head, sharp-toothed, snarling jaws, a pair of swept-back tendrils and yellow eyes, a body with grey-purple flesh, with green, bristle-lined plating partially covering its body and loops over each shoulder, three-fingered claws, digitigrade legs and raptor-like feet.)

"Yikes, I've never seen anything that ugly since the bokoblins that were on the beachside in the east." Rozel exclaims, repulsed by the space pirates appearance.

"So, you haven't seen this creature?" Link asks with disappointment.

"No, can't say that I have, son."

"Hmm, maybe it's not relevant, but a few months ago one of the kids said he saw some 'bogeyman' that came out of the sea and he won't stop talking about it." Numar speaks up. "I think it was Zuta, Sebasto's kid."

"Would he be available to talk to?" Samus asks.

"Yeah, it's almost sundown, he's probably out and about now. If want to ask him, better do it now."

"Alright, thank you both for your hospitality. I'll come back for a longer visit when it's over. Come on ladies, no time to waste." Link hurriedly walks out to find Zuta, Zelda and Samus thank the two as well and follow Link outside. Just as stated, Zuta is out on the grassy fields looking for beetles. "Zuta! Hold on a minute!"

"Huh? Oh Mr. Link, hi!" Zuta, a brown skinned boy with a knot top, blue shirt and brown shorts, runs up to Link and greets him. "What's up?"

"Hi buddy, listen; I heard from Numar that you saw a 'bogeyman', can you tell us about it?"

"Yes, it probably looks like something we're searching for. Maybe you've seen it?"

Upon hearing this, Zuta's expression goes from excited to annoyed. "Great, it's not enough that the other kids pick on me because of it, now you and even the princess are making fun of me too?"

Link tries to explain himself over Zuta's accusation. "No, that's not what I-"

"Look, I know what I saw. Don't make fun of me." Zuta walks away in a huff.

"Little one, please! We meant no offense!" Zelda reaches out to try and stop him from leaving only for Samus to catch up to Zuta.

"Hold one a minute kid. I'm sorry if you thought we were bullying you." Samus bends her knees to be at eye level with him. "Let's start over; I'm Samus." She extends her hand and smiles sweetly.

Zuta's expression softens at Samus's friendliness and he slowly extends his hand and shakes hers. "Hi, I'm Zuta."

"I know that the other kids made you sound like a liar, but this bogeyman is probably a very dangerous monster that could hurt a lot of people if we don't find it. If you tell us anything about it, we can stop it from doing anything bad. Don't you want to help us save everybody and be Lurelin Villages hero?" Link and Zelda look on in surprise at Samus's friendly approach. Immediately after, Zuta eagerly whispers some things to Samus and upon finishing, runs off back to the village, happily waving to all three of them and grabbing a branch to swing it like a sword while shouting "look out, here comes the village hero!"

"Alright you two, according to Zuta, he saw the monster run off towards the beach to the east but didn't follow it." Samus explains. "According to his description, it looks like it is, in fact, the space pirate."

"You seem to have a way with kids, I'm impressed." Zelda comments.

"I've been around a lot, you pick up some things." Samus smiles ear to ear, causing all three of them to laugh.

* * *

 **Palmorae beach**

"Alright, what are we looking for?" Link asks, having reactivated his suit.

"Anything out of the ordinary. We're probably in its campsite." Samus answers and the three separate to look for anything suspicious. Zelda, having opted to search the rocky area of the beach, presses up against the rock wall to not fall into the water and falls through the wall.

"What is this?" Zelda wonders aloud while rubbing the back of her head. "It was a fake wall!" Zelda rushes out of the wall and calls out to the others, who rush to her position and see the fake wall, revealed to be a holographic projection from a device at the entrance. Samus crushes said device, revealing a cave that (according to Link) was never here before. Undeterred, the three venture inside and find a makeshift campsite, including the skiff (which is essentially a flying platform with four hovering apparatuses underneath and a beak like shape at the front), several rations, a campfire and (more importantly) a transportable database.

"Yeah, this is the place alright." Samus says as she grabs the database and the two move in to see its contents. "Now, let's have a look."

* * *

 **Personal data log: while searching for more of our installations, our ship was attacked by a Galactic Federation battleship. Though many of us were killed, a few (myself included) managed to escape. I found the nearest planet to escape to, but my ship was damaged by what I could only describe as a "purple thunderstorm" and it crashed onto a small island. After managing to escape the wreck and finding refuge, I tried making contact with the others, but an interference of unknown origin is blocking all communication outside the planet. I may have to find out more about this world tomorrow, for now I should tend to my wounds and try to establish communication through other means.**

 **End of data log entry.**

* * *

"Purple thunderstorm? He must've meant Calamity Ganon. While I was fighting that, he must have flown by." Link says in realization.

"Then, he came here because he was escaping your version of local law enforcement. Yes?" Zelda asks.

"Yes, that solves that mystery." Samus answers Zelda's inquiry while scrolling through the entries. "But, we have one that's still pending; after the fifth entry, he stopped adding more, why? Where did he go?"

"Something seems to be going on." Zelda deduces and the others nod in response. Before they can investigate any further, the Sheikah Slate begins to glow, indicating an alarm. Zelda pulls it off her belt and answers the call.

"If anyone can hear this, please respond." A woman in clear distress calls out.

Not wanting to expose Link or Zelda to a potential trap, Samus answers in their stead. "Identify yourself."

"My name is Jerrin of the Akkala Ancient Tech Lab, my husband and I escaped from there after it was destroyed by the Yiga and their monsters. We're holed up in Tarrey Town, but we fear that they will come for it as well. Please, we need help."

"Jerrin? It's me, Link. Did you say the lab was destroyed?!" Link answers in concern.

"Link? My boy! It's me, Robbie! Yeah, those uncultured pigs did a number on it! Not even my poor Cherry made it out of there…"

"Don't worry, we're coming to you now! We're coming in a large flying machine, we'll be there soon." Zelda reassures as they walk out of the cave and Samus uses her command visor to bring the ship around. Upon boarding the ship, they continue to speak with Robbie and Jerrin, who told the residents of Tarrey Town that Link and the princess would be arriving, causing them to want to speak with Link.

"Huh, no wonder we never saw you in Hateno. You were off gallivanting in a flying ship, too busy to say hello." Bolson, head of Bolson construction, quips to Link.

"Hahah, good to hear from you too Bolson. I was wondering why I didn't see you there a few days ago. You went to visit Hudson and Rhondson I bet?"

"Yep, I think I should always make time for the happy couple. Don't you agree, Karson?"

"Of course! Everyone from Bolson construction is like family!" Karson, one of the more well-known workers, excitedly agrees.

"You've got some very colorful friends, my boy." Robbie comments.

"Heh, they're pretty cool, aren't they?" Link comments.

"It was kind of them to offer you sanctuary." Zelda gratefully comments. "When we get there, we'll get this mess straightened out. Don't worry."

"What do you mean 'when you get here'? I see your ship already, Linky boy!" Bolson exclaims while waving at a different direction.

"What?" Samus asks in confusion.

"Yeah, you said you'd be coming in a flying ship. It's a greyish colored one, right?"

"No, we're still on the way-"

"WHAT THE HELL?!" Robbie is interrupted by several explosions in the background.

"Robbie, what's going on?!" Zelda shouts in panic.

"Everybody, get away from it!" Bolson shouts to the residents.

"Such power…" Jerrin whispers in fear.

"Oh Gods!" Karson shouts in horror as the connection is finally lost.

"Robbie! Bolson! Anyone?!" Link shouts in vain.

"Virginia, double time!" Samus gives the order to increase the speed to reach Tarrey Town.

* * *

 **Tarrey Town**

The ship lands just outside of the bridge leading to Tarrey Town, which is in flames. The three exit the ship and desperately race to find anyone. They then see Karson and Greyson (a Goron worker) being flung across the town.

"Karson! Greyson!" Bolson shouts from behind a ruined house.

"Stay there boss! It's too dangerous!" Karson struggles to get up to attend Greyson. From above, Fyson (a Rito merchant) shoots several bomb arrows at the assailant, only for his wing to get shot by a plasma blast.

"Argh, my wing!" Fyson exclaims in pain after falling down. Hudson (the founder of Tarrey town) rushes out to drag Fyson away from the assailant and bring him to safety. "I got you buddy, you'll be alright."

"Bring him here! It's alright now, let me see your wing." Rhondson (a Gerudo seamstress and Hudson's wife) applies a salve to ease the burn on Fyson's wing.

"Everyone, over here!" Link shouts to the residents to head to the path that Samus cleared with her ice beam. "Get to the bridge!"

The people start shouting in praise as they help the wounded on their feet, but are interrupted by metallic footsteps. From the raging fires emerges a large behemoth of a machine with flaming claws and a frill like structure in the front.

"What is that thing?" Zelda asks in fear.

"It can't be…" Samus exclaims in disbelief.

"Ah, there you are, Samus. You didn't forget about your old friend Ghor, did you?! Hahahahah!" Ghor insanely shouts as he readies to attack the trio.

 _To be continued_

* * *

 **Authors note: More mysteries! Sorry for the long wait, it took me a while to get this chapter down to the way I'd like it, but here it is. Now, time for the action to pick up again in the next chapter. See you soon! :)**


	12. Chapter 12 Tragedy in Akkala

**Chapter 12: Tragedy in Akkala**

 _'Tragedy should be utilized as a source of strength.' No matter what sort of difficulties, how painful experience is, if we lose our hope, that's our real disaster." -Dalai Lama XIV_

 **Answering the distress call from Tarrey town, the trio makes it to the settlement only to see it engulfed in flames. Although the people are still alive, their attacker is still in the vicinity. Even more unsettling, he is revealed to be Ghor; Samus's old compatriot who should be dead.**

"Ah, there you are, Samus. You didn't forget about your old friend Ghor, did you?! Hahahahah!" Ghor insanely shouts as he readies to attack the trio. "It seems you've found two more to kill!"

"Ghor! How are you still here?!" Samus shouts.

"You know him?" Link asks while brandishing the Master Sword.

"Enough talk already! I want to settle the score!" Ghor aims his turrets and fires a volley of plasma shots. Link grabs Zelda and jumps out of the way while Samus jumps up and shoots a super missile, which Ghor deflects with his shield generator. After getting Zelda to a safer distance, Link runs forward and tries to slam down the AKEB charged master sword on Ghor's face, but he moves to the side and swats Link away. While distracted, Samus jumps on his back and shoots the wave beam at the back of his head. Annoyed, Ghor starts spinning around, causing Samus's grip to loosen and fall off, allowing Ghor to grab her by the left leg. While quickly rotating the top half of his mechanized body, Ghor throws Samus into one of the burning buildings, collapsing on top of her. Now, Ghor turns his attention to the terrified townspeople.

"Where are they?!" Ghor shouts in a monstrous robotic voice. "Where are the soldiers?! Where are you hiding them?! I will burn you all to ash if you don't tell me- aahh!" Ghor is suddenly cut off from his tirade by a fireball to his face.

"Leave them alone!" Zelda angrily shouts with flaming hands.

"You little pest!" Ghor shoots several missiles at her, which Zelda hits with another fireball to have them detonate in midair. As the smoke clears, Zelda is nowhere to be seen. Ghor looks to his front and side to side, until he hears a whistle from behind and turns around to see Zelda aiming an ice arrow (with the Lynel bow) at his face, which she fires point blank. "Argh, I can't see!" This gives Link enough time to run up and slam his charged master sword onto Ghor's chest, damaging his chassis significantly. Before he can retaliate, Ghor screams as electricity surges through his body and he falls to his knees. Samus jumps up from behind him and regroups with Link and Zelda (removing bits of rubble from her armor).

"If you drop another house on me, I'm going to lose it." Samus exclaims in wide eyed anger.

"Samus, the longer he stays here, the more damage the town takes." Link says while moving to her left.

"Yes, if only we can get him to fall down to the water somehow." Zelda comments.

"Anyone got any ideas?" Samus asks while aiming her cannon.

"I have one; BURN!" Ghor shoots a ray of plasma at the group, who barely manage to avoid. "Fine, I'll turn this whole town into a smoldering pile of ash after I kill you!" Ghor continues his onslaught by shooting several plasma blasts from his cannons, damaging more buildings in the process. Samus fires her seeker missiles, but these prove to only be a minor hindrance, stopping his attack at the most. Link slashes at Ghor's chest with his electrically charged sword, stunning his plasma stream and allowing Link to land a heavy blow to Ghor's main body.

"Leave these people alone! They've done nothing to deserve this!" Link angrily shouts.

Ghor recomposes himself from the impact, looks at Link then back at the residents hiding in a mostly undamaged house. He then chuckles sinisterly before speaking up. "These people mean a lot to you, do they not?" Ghor aims one of his arm cannons at the residents and threatens to open fire on them. "Then let us see how you fight with their blood on your hands!"

"You coward!" Link runs up and grabs his cannon, pointing it upward and causing it to shoot towards the sky. While Link grapples with Ghor, Zelda shoots ice arrows at the compromised areas on his armorsuit and Samus tries to hit those frozen points with missiles.

"Bah! This is getting old, begone!" Ghor jumps into the air (Link is still holding on to his claw) and lands with enough force to create a shock wave, knocking Zelda and Samus away. Ghor turns his attention to Link, who fruitlessly tries to stab him, and punches him to the ground with his other claw. Zelda is the first to regain her composure, in time to see Ghor take aim at the residents. They prepare for the inevitable and something inside Zelda has her running towards them to intercept the blast; as she jumps in front of the plasma stream, the symbol of Nayru appears on the back of her right hand and a transparent blue diamond shaped barrier envelopes her. The stream makes contact with the barrier and redirects it back at Ghor, who takes the full force of the blast, pushing him a few feet from the edge and seriously damaging his armorsuit.

"Argh, how did you do that?! What technology do you have hidden?!" Ghor angrily shouts as he removes his malfunctioning frill that obscures his sight. Link and Samus rejoin Zelda and, upon witnessing her new power, they come up with a plan to get Ghor to fall down and spare the town any further damage. As they finish preparing their plan, Ghor completed repairs to his mobile functions, but was unable to repair his shield generator, remembering that Samus had shorted it out earlier. Link and Zelda look at Samus, who nods in acknowledgement and runs off.

"What is this? The great Samus Aran running from a fight?" Ghor comments while readying his cannons. "What are you playing at?"

"I just sent her to find the soldiers, I figured out where they are. She's going off to offer assistance." Link replies while entering a fighting stance. "In the meantime, you'll just have to contend with us."

"In other words, you are not going anywhere." Zelda sternly remarks while glowing with power.

"You are about to regret keeping me from my mission!" Ghor attacks the pair and Link activates Daruk's Protection to deflect his physical attack, giving Zelda time to shoot a bomb arrow at Ghor's face, causing him great pain.

"Come on, you can do better than that!" Zelda, uncharacteristically, taunts Ghor. In response, he fires several plasma missiles from his back, which Link shoots down with a skyward strike.

"Seriously, they sent you on a mission when you can't even take on a pair of young adults? The Yiga must be very desperate." Link also joins in on the jeering.

"Impudent little whelp, who do you think you're talking to?" Ghor angrily says in a quiet voice.

"Not a great warrior, I'll tell you that much." Zelda says in a derisive tone.

"Shut your mouth!" Ghor shoots several blasts at the two, which they dodge to the side, running behind a ruined house. "Come out and fight, you little rats!"

"Over here." Link shouts from behind, slashing at Ghor's back, damaging one of his propulsors. Ghor spins around to try and catch Link with his claws, but he ducks down and slashes at his legs. Angered, Ghor settles with wanting to crush him with his claws, which Link avoids with no effort.

"Stand still!" Ghor shouts.

"No." Link calmly says and charges his sword with fire, slicing off Ghor's left claw. Finally pushed to blind rage, Ghor charges his plasma cannon on the armorsuits chest. "There we go; now!"

"Got it!" Samus answers via her communicator and starts running down the hill to the northeast of the town, charging her speed booster.

"DIE!" Ghor blasts the fully charged plasma stream at Link, who ducks down and lets the stream hit their trap; Zelda.

"The funny thing about rage is that it makes you lose sight of everything else." Zelda says with her barrier activated, which once again redirects the blast at Ghor.

"NO!" Ghor takes the full blast once again, forcing him back towards the edge. Link follows up with an AKEB charged slash, forcing him back even further. Link ducks down and Samus shinesparks (speed booster powered jump) above him, slamming into Ghor and finally causing him to fall down the edge. Ghor screams as he falls down into the water. The three reach the edge of the town.

"We did it!" Zelda ecstatically says. "The townspeople are safe."

"Yes, the plan worked perfectly." Samus breathes a sigh of relief. "I'm sorry about this again, Ghor."

"I never knew that you had such a condescending side to you, Zelda." Link jokingly comments.

"Well, the idea was to get him angry. Don't expect me to look down on others in the future again."

"Alright, you two relax for a bit; I'll put out the fires." Samus says in a glum tone while recalibrating her ice beam. Just then, Zelda stops her to ask how she knows Ghor. He was one of three other bounty hunters assigned to assist the Galactic Federation in stopping Dark Samus originally. When finally asked why Ghor was so obsessed with wanting her dead, Samus faces away from Zelda and answers with shame present in her voice; "I killed him…All three of them..." Zelda looks at Samus walk away with melancholy before returning to Link, who wants to check on the townspeople. Though, one thing bothers her; if she killed Ghor, then how is he even here? Before anything else can be said or done, a transparent blue tentacle wraps itself around Link and drags him down to the forests beneath Tarrey Town.

"Link!" Zelda shouts, alerting Samus from putting out the rest of the flames.

"What's going on?!" Samus runs up to see what the ruckus is.

"Something grabbed Link! I think it was Ghor!"

"Come on, hop on my back!" Zelda holds on to Samus and they jump down to the woods.

* * *

Link is thrown against some ruins and Ghor jumps out from the water, having entered hypermode and a severely damaged armorsuit.

"You little human meat bag! I'll tear you apart!" Ghor shouts in fury as he extends several phazon tentacles to the damaged guardian stalkers and brings them to him. Once collected, Ghor superheats the guardians and molds them into a new suit with long arms (hands with five claws and lasers on the palms) and legs (spear like instead of regular legs), another pair of lasers on each shoulder, four spider like legs on his back and a whip like tail.

"What are you?" Link says in a worried tone.

"Time to die, Link!" Ghor aim his palm, firing a laser which Link blocks with his shield, pushing him back. Seeing that he is still standing, Ghor runs to him (eight legged stride) and slashes the tree that Link slammed against, just barely missing him.

"This is not easy. The phazon made him stronger." Link says, getting back on his feet after dodging his claws. Ghor quickly grabs Link by the leg with his tail and dangles him upside down while facing him directly.

"I must admit; these machines, while primitive, serve their purpose well. How I would've enjoyed seeing them at their maximum a century ago." Ghor then tries to sink his claws into Link's chest, but is stopped by an arrow shot from Zelda at Ghor's tail. Link lands and uppercuts his chest, making Ghor back off briefly.

"Got here just in time." Samus says with relief.

"Link, are you alright?" Zelda asks with concern.

"I'm still standing." Link answers directly.

"Not for long…" Ghor runs at the group and Zelda uses her barrier to deflect him, giving Samus time to shoot power beam blasts at his chest, which do nothing. Link concludes that it's his new armor made of guardian parts; made to be almost impervious to most weapons. Ghor jumps forward and shoots Samus with a laser beam, sending her back a few feet and damaging her suit slightly. Link charges his sword with fire and slashes across Ghor's chest in an attempt to reach his main body, only barely scratching the suit. Zelda has Link back away before Ghor can retaliate and shoots a pair of bomb arrows, which once again do little against the guardian enhanced armor, but manages to stun him momentarily.

"Link, we need a new strategy! His armor is too strong!" Zelda shouts.

"I know! But what can we use?" Link answers in desperation.

"Link, catch!" Fyson flies down (with difficulty due to his injured wing) and drops a pair of bags at Links arms, he quickly open the first one and finds several bundles of ancient arrows which he gives half to Zelda and puts the other half in his quiver. "Robbie said you might need those against the monster, the other bag is for the big guy in the orange armor! Good luck!" Fyson flies back to town just as Ghor regains his composure.

"Do not interfere!" Ghor aims one of his shoulder turrets at Fyson as he flies away, but Zelda shoots an ancient arrow at it, causing him to lash out in pain and permanently damaging the turret. Ghor observes his damaged turret and tears it off when he realizes that it will do him no good.

"Samus, here!" Link tosses the other bag to Samus, who just recovered from Ghor's attack. She opens the bag and sees a rod with intricate designs and a long handle. Upon grabbing the handle, the rod activates small, rotating, blue blades around its edge. Ghor retaliates by jumping forward and grabbing Zelda by the torso and squeezing her with both hands to suffocate her, causing Zelda to scream in pain. In response, Link shoots an ancient arrow at Ghor, blasting off one of his back legs and loosening his grip. Zelda manages to free one of her arms, with which she tries to reach out to Ghor with her red hot palm (shooting a fireball from such a close distance would catch her in the blast radius). Before Link can ready another arrow, Ghor grabs him with his tail and drives one of his legs into his ankle.

"Aaahh!" Link shouts in pain as he grabs the leg to keep it from digging deeper.

"That's enough!" Samus angrily shouts while revving the ancient bladesaw. Using the boosters on her back, Samus closes the distance and runs the blade over Ghor's arm, damaging several circuits and causing him to retreat, removing his leg from Link's ankle. Link fights through the discomfort and shoots a pair of ancient arrows at Ghor's chest, weakening him and allowing Zelda to place her palms on his head.

"RAAAAAHHHHH!" Ghor shouts in pain as Zelda's flaming hands press down on his head. Just then, Zelda sees an image of Dark Samus's visor over Ghor's face and his body covered in blue chains.

"What is this? Where are we?" Zelda wonders aloud while realizing that they are both in a dark, empty space. Ghor looks up at Zelda from his spot with his eyes (or rather optics) covered by Dark Samus's visor and speaks in a strained voice.

"Help me…"

"What?" Zelda couldn't believe what she was hearing; first Ghor tried to kill her and her friends, and now he was asking her for help. Taking in Ghor's appearance in this dark space made her realize that she's in his mind. Finally, she comes to the realization of Ghor's plight. "You're trapped…"

"Zelda!" Link shouts, waking Zelda from her trance, and hits Ghor with another arrow, finally causing him to release Zelda. Samus rushes towards Ghor while Zelda goes over to Link to tell him what she saw.

"Link, he's not doing this of his own free will!"

"What are you talking about?"

"He's trapped! We must release him from the grip of Dark Samus!" Before any more can be said, they're interrupted by Samus slamming into a nearby tree and Ghor running at them at full speed, having reactivated hypermode. Link puts their conversation on hold and hits Ghor with another ancient arrow, but due to hypermode, it does very little. Zelda restrains Ghor with her power and tries to reason with him, but he merely shouts in rage due to his augmented power. Samus runs forward, shooting several nova beam blasts and then jumping on to Ghor's chest and pressing the bladesaw onto it, whittling away his armor little by little.

"Link, those arrows won't be enough! Hit him with a phazon and ancient arrow at the same time!" Samus shouts amidst the sound of grinding metal. Link complies and arms the two arrows, Samus jumps off and he lets the arrows loose, disrupting hypermode and damaging his armor. Link takes the opportunity land a flurry of slashes on Ghor while he's both disoriented and restrained, causing Zelda to yell in protest.

"No Link, you can't kill him! He needs our help!"

"We can't help him!" Samus steps in to retort. "Complete corruption is irreversible! There is nothing we can do because there is nothing to save!" Samus arms her annihilator beam and points it at Ghor. "This is the only way to end their suffering. I'm sorry…" Samus shoots a volley of sonic blasts at Ghor's now brittle armor, shooting it off piece by piece. Ghor falls to the ground and Link alternates between slashes and shield bashes to reach his main body as Zelda watches on with sorrow over being unable to help free Ghor. Link finally slashes off the ancient armor, exposing Ghor.

"Now, finish it, Link!" Samus shouts having stopped her suppressing fire. Ghor regains his composure in time to see Link prepare to impale him.

"Raahh!" Link charges the sword with fire and thrusts it into Ghor's chest while Zelda looks away. Ghor lets out several strained groans as his new armorsuit crumbles away, Link removes the sword and backs off as Ghor floats in the air and a wraith like apparition of Dark Samus appears from within Ghor, shocking Link and Zelda while Samus looks away in sorrow.

"You have failed me…" The wraith whispers sinisterly. "Return to whence you came…"

"No...Not again! Please no!" Ghor shouts in panic. "I don't want to return to that darkness!" The wraith begins to laugh quietly as it begins to absorb Ghor. Link, having his opinion of Ghor slightly changed by his pleading, softens his expression.

"Can't we do something about this?"

"There's nothing we can do. He's gone." Samus says while clenching her fist. Zelda, being tormented by his shouts, gives in and rushes to Ghor. "Zelda, get back here!"

"What are you doing?!" Link shouts in alarm

"Leave him!" Zelda puts up her right palm and summons her power, enveloping her and the wraith in a golden light. The wraith begins to convulse and screech as the others (including Ghor) look on in confusion. "Foul monster, begone!" The wraiths black color quickly turns gold as it begins to disintegrate and, with one final screech of agony, bursts into millions of particles that disappear into nothingness. Zelda falls to her knees and tries to catch her breath as Link and Samus gather around her.

"Are you alright?" Samus kneels down and puts her hand on Zelda's back. "What exactly did you do?"

"I thought I could banish it, it seemed to be made out of darkness." Zelda says, taking into account her powers abilities. The look up to see Link taking aim at Ghor. "What are you doing?"

"Something is happening.' Link answers as Ghor floats in the air, soon his PED attachments wither away and he's left with his regular body (a thin humanoid shape with metal plates covering the outside of his legs, three fingered arms also covered by exterior metal plates, a metallic breastplate covering what may be organic components and a cylindrical, dome shaped head with red optics and an expressionless mouth). He floats down and to everyone's shock becomes surrounded by green ethereal lights.

"Well, this is a new and unexplained sensation." Ghor calmly says, taking in his surroundings and ignoring everyone else entirely.

"Ghor? Is that really you?" Samus stands up and asks in disbelief.

Ghor looks to their direction and speaks up. "Samus. It is good to see you again, all things considered."

"So, you are the _real_ Ghor?" Zelda asks, unsure of what will be his response.

"If by real you mean _unaltered,_ then yes I am. Now, I believe thanks are in order; little one, I thank you for freeing me from Dark Samus." Ghor extends his hand out to Zelda, who takes it while being wary of his pointy fingers. "Now, I believe I know your next question; how did I get here?"

"That is right, I mean Samus told us you were…" Link comments, unsure if he should finish his sentence.

"Dead. You're right about that. Very well, I will explain it to you." Ghor explains that at the time of his death, Dark Samus absorbed his essence (or soul) into her being and brought him back by restoring his body through genesis chambers, large womb like structures used to grow infant leviathans before they are sent out to other worlds to spread phazon. Dark Samus had managed to create several smaller ones and Ghor was one of their occupants.

"So, that's how you came back." Samus says. "And what have you been doing before this?"

"Mostly I've been overseeing the mining operations at Death Mountain, but then I was sent to find the soldiers here when these Yiga people couldn't finish them off. That is the reason I was, regrettably, attacking those people in that town."

Link and Zelda are alarmed by this revelation; the soldiers that they (specifically Link) stationed here are being threatened and if Ghor was overseeing some sort of mining operation on Death Mountain, what does this mean for the Gorons? Ghor explains to them that they have been enslaved and used to mine black phazon crystals, a strong substance used to make weaponry and armor out of the product that comes from refining it called phazite, which have gathered in enormous amounts in the Eldin region. He also explains that the soldiers stationed in Akkala caught wind of this and motioned to stop the Yiga, but they were outnumbered and attacked by their forces. They retreated to the still damaged Akkala citadel (their temporary outpost), but that was the last Ghor heard anything about it before being sent to find any stragglers.

"Personally, I suggest you head to Eldin to stop the mining of crystals and free the Gorons from their torment. But you must hurry; the phazon has made the volcano very unstable. I doubt there will be much time between now and an eruption of phazon charged magma."

"I want to search for my troops first, how much time do we have before we can expect an eruption?" Link asks with concern.

"I cannot give you an exact answer. I never gave it any thought while I was _lesser._ But if there are other people who need your aid, then they should take priority. Well, this is all the information I can give you now. You must all hurry along and stop this madness."

"Ghor, thank you for all of this useful information." Zelda gratefully says. "I'm glad we could help you as well."

"No thanks are required, I am simply glad that I can atone for the damage I have wrought."

"We won't forget this, Ghor. Thank you." Link respectfully comments.

"Ghor, I am sorry for everything that time on Elysia." Samus laments over their last encounter.

"It was unavoidable Samus; there is no need for any forgiveness. I'll have my justice when you finally blast that blue harpy to dust." Ghor says with a tinge of spite in his words. "For now, I wish you all luck." Ghor waves goodbye as he disappears and upon leaving (snarkily telling the "lady voice" that he hopes she has machines in her realm), Samus thanks Zelda for freeing her old compatriot, to which Zelda smiles at. The three first decide to return to Tarrey Town to check on the townspeople. Upon reaching the town, the first people to greet them are Bolson and Robbie, who thank them for saving the majority of the town and all of the residents. Before they say anything else, the two lead them to a basement in one of the houses, because "there's someone they need to see". On a side note, Samus breaks away to search the citadel for any clues on the soldiers whereabouts (Zelda had told her that the Akkala tower is on top of the citadel, so it isn't difficult to find), all in order to save as much time as they can.

* * *

 **Basement underneath the inn.**

Robbie, Bolson and Hudson are happy to see that he and Zelda are (for the most part) alright. Afterwards, they enter a room in the basement where the injured (Fyson, Greyson and other townspeople) have been brought to recover and overseen by Rhondson and Kapson (an elderly Zora priest).

"Link, good to see you again." Kapson walks up and pats Link's shoulder. "But, I only wish you could've come at a better time, we're not exactly at our best at the moment."

"Well, it's not our fault that some big metal doohickey crashed our happy welcome." Bolson says with a scoff.

"Regardless, what is important is that you are all safe now." Zelda comments.

"Mom! Dad!" Granté, a young Sheikah man with the usual Sheikah attire and dark blonde hair that covers his left eye, runs down the stairs and embraces his parents, Robbie and Jerrin.

"Granté! Thank Hylia you're safe!" Jerrin excitedly says while hugging her son.

"Son! Where have you been?" Robbie asks, happy to see Granté.

"I was just taking a walk to get some fresh air, after that I thought I should visit the lab, but it was destroyed. I wanted to see if you two were nearby, then I saw the fight in the woods and Tarrey Town in flames, so I went there."

"Well, we came here thinking that you were somewhere in town. But we couldn't find you." Jerrin answers. "But at least we're together again."

"Granté, good to see you again." Link happily says as he pats Granté's shoulder.

"Link! I should've known you'd be the one who helped the town." Granté says, happy to see his friend. "Thankfully, you and your buddies were here to stop that machine."

"I'm glad we got here in time. I can't bear to lose any more friends." Link comments with relief. "Anyway, I think there was something you wanted to show us?"

"Ah, that's right. There's someone who wishes to meet you. Rhondson will take you to them." Robbie cuts in as he leads them to Rhondson.

"Sav'aaq Link. Sav'aaq your Highness." Rhondson gives the usual Gerudo greeting to the two. "Are the two of you feeling alright? We could wait awhile before meeting the ones that summoned you."

"No thank you, we shouldn't waste anymore time. Let this person know that we're ready to speak with them." Link says directly.

"Very well, then they will see you now." Rhondson says as she opens the door to the other room, leaving Link and Zelda surprised.

* * *

 **Outside the Akkala Citadel**

"Do you see anything?" Samus asks cautiously as she approaches the citadel.

"Negative. No vital signs detected in the vicinity." Virginia reports. Upon reaching the (reconstructed) bridge, she sees several dead bokoblins, all of which were corrupted. Approaching the entrance to the citadel, Samus's alarm points out a sudden increase in phazon energy as the door blasts open and an Elite Pirate tackles her to the ground. Samus jumps back to her feet and retaliates by firing several missiles at its head, but it blocks them with its fist. She follows up by striking it with the bladesaw, slashing its chest and causing it to recoil. When she tries to strike again, the elite pirate stomps her away and attacks her with its retractable bayonets, Samus slides on her back to dodge its slashes, rolls beneath its legs and then shoulder bashes it in the back before raining a hail plasma beam shots to penetrate its armor while it is fallen. Using its shockwave generators (within its fist), the elite pirate sends waves on the ground, knocking Samus off her feet and allowing the pirate to shoot her away with its shoulder cannon. She lands on her feet and quickly blasts a super missile at its chest, cracking its armor further and causing it to rage as it charges towards her. She jumps over its head and shoots a volley of seeker missiles down, injuring it further. Landing behind the pirate, Samus turns around and to her shock, the elite pirate convulses as several phazon growths form along its arms, shoulders, upper back and right side of its face.

"The phazon level increased significantly, it has mutated into a much more powerful form. Exercise extreme caution." Virginia gives her report.

"Copied." Samus charges forward, sliding underneath the pirate's incoming fist and shooting a blast of ice at its face. While it's distracted, Samus sweeps its legs with her own to knock it down and then shoots nova beam shots at its chest. After a few shots, it's shown that its new epidermis is much stronger than before and the pirate gets up and punches Samus away. She gets back up and tries to slash it with the bladesaw, but it grabs it (while the blades are spinning) and crushes it without a single scratch on its palm, much to Samus's horror. Dodging a left hook, Samus jumps back and assesses the situation.

"I need a different approach."

"If I may, using your aeion tanks may prove useful against it." Virginia offers her advice to Samus.

As this is being said, the elite pirate charges at full speed towards Samus. "Activate it now!" The elite pirate slams its fists down on Samus; it lifts them to see that she is no longer there. Its search is interrupted by an unknown attack from behind it, followed up by more shots from different directions. Brought to its knees, the pirate tries to recover from the unknown assault and sees Samus appear out of nowhere.

"Phase drift deactivated." Virginia reports, having stopped the flow of aeion through the suit ( **AN: phase drift allows Samus to slow down time, to everyone else it's as if she's moving at blinding speed** ) and focuses it on the arm cannon, giving it a yellow glow. "Beam burst activated and fully functional."

Samus selects the plasma beam and, with the beam burst, launches a rapid fire blast at the elite pirate's chest, whittling away its armor skin and destroying its chest. As its heart and other organs are destroyed, the elite pirate gives one final exhale and falls to the ground dead. Samus lowers her smoking arm cannon, deactivates the beam burst and breathes a sigh of relief. "Finally…"

"The aeion tank is at 84%. You still have plenty more uses left." Virginia states after measuring the remaining aeion.

"Good, let's only use it for extreme circumstances. Now, let's find any clues as to the soldier's whereabouts." Leaving the rotting carcass of the elite pirate behind, Samus enters the citadel and is left horrified by the scene she witnesses.

"Samus, I believe that the elite pirate wasn't originally meant for you. I count 36 in total…" Virginia says after counting 36 "objects".

"Virginia, I need to speak with Link…"

* * *

 **Back in the basement of Tarrey Town**

"Sir Link! Thank Hylia, you and the princess are unharmed!" The unnamed soldier, the person who wanted to see him, says with relief.

"You're one of the soldiers stationed here! I'm glad to see one of you at least." Link says while shaking his hand.

"Yes sir. I'm lieutenant Stannis of the Akkala Guard. I'm sorry that we're not all present and accounted for." Stannis, a young knight with short brown hair and the usual soldier armor, says while motioning over to another injured knight on a bed. "As you can see, it's just me and commander Mormont, and he's hurt bad."

Link and Zelda turn their attention to commander Mormont, an older man with thinning grey hair, a short beard and a gruff voice. On better inspection, they also see a large wound on the left side of his abdomen.

"Sir Mormont, can you hear me?" Zelda quietly asks.

"No…" Mormont says without opening his eyes. "We must hold the line…"

"What is he saying?" Link wonders aloud.

"Stand tall, men! We must not let them through!" Mormont shouts in desperation as Stannis keeps him from getting out of bed and exacerbating his condition.

"He's been doing this since we escaped from the citadel. I think it traumatized him." Stannis somberly says.

"Stannis, what happened? Where are the others?" Before Links question can be answered, an alert sounds from his suit (specifically, a light on his right arm). Link activates it and a holo-screen appears from his arm with Samus appearing in it.

"Link, your auxiliary communicator works. Good." Samus says without a hint of surprise, or any other emotion for that matter. "First off, how many soldiers were stationed here?"

"I had 52 sent here for reconnaissance and aid to the locals. Why?"

"...I counted 36." Samus moves the camera to face the interior of the citadel and Link and Zelda are left speechless as they see 36 soldiers strewn all over the place. "I've confirmed it; they are all dead."

"Hylia above, how did this happen?" Zelda whispers in horror.

Stannis leans against the wall, facing away from the two, and recounts everything to them; when the blue barrier rose from Death Mountain, they were stationed at the citadel with the previous assignment of watching over the region for monster encroachment. Unsettled by its sudden appearance, commander Mormont sent 2 scouts to assess the situation. One day later, the scouts returned with news that the Yiga had occupied Goron city and the mines from one of the Gorons that managed to get away. He told the scouts that the Yiga and several unusual bokoblins and moblins attacked their homes, enslaved the captives and forced them to mine these bizarre crystals, as well as using these objects that this blue armored stranger sprouted from the ground and had them hatch these monsters to track down any stragglers that got away. Stannis was sent with a small band of troops (on horseback) to confront the Yiga, but they were intercepted before reaching the entrance to the city. Facing their overwhelming power, they were forced to retreat back to the citadel. Unfortunately, when they were planning a new strategy, the Yiga had tracked them back and attacked them with one of those monsters (which they used to break down the door) at their weakest.

"They were trying to snuff out all resistance; we were targeted for wanting to help citizens in need. For that, they attacked the citadel." Stannis says with remorse.

"And that is when…" Zelda begins to put the pieces together.

"I saw my comrade's fall, one by one. Commander Mormont did his best to lead and save us, but he got hit. Badly." Stannis looks at commander Mormont, still struggling with the pain of his injuries. "I was left with no choice, I took the commander and told the survivors to abandon the citadel, but a blast from the monsters cannon separated us from the others. They went one way and we went another, eventually finding Tarrey Town. The people took us in, and we've been hiding here ever since."

"I knew it; they left the elite pirate here just in case any of the survivors decided to come back." Samus concludes.

"And I'm the one who sent them here in the first place." Link says with regret and sadness. He looks at the two survivors and then at Zelda (who has an expression of sadness as well), before regaining his determination. "We must go to Eldin, the Yiga are clearly doing something nefarious with these crystals and must be stopped. We're the only hope for the Gorons now…" Link says and Zelda nods in response. "Samus, how fast can you get back here?"

"In about 3 minutes."

"Good, we'll be ready by then."

"Now then, what will the rest of you do?" Zelda asks.

"I talked to Hudson; we agreed that it would be best to leave Tarrey Town for the time being." Robbie answers. "We need to leave all at once, so with Bolson and the others, we'll make a type of carriage using wood from the houses and parts from the guardians down there. When Fyson is better, he'll go to the south Akkala stable to borrow some horses."

"Excellent. It would be in your best interest to find a safer place for now." Zelda says before looking at Hudson, who has a disappointed look on his face. Rhondson walks over and holds his hand, making him face her and try to smile. "There now Hudson, I know that this is difficult for you; you built this town from the ground up, but it isn't goodbye, it will thrive again. I guarantee it." Zelda puts her hands on his shoulders and gives him a reassuring smile. The others proclaim that they built the town from nothing and that they'll do it again, Bolson in particular reminding him that he and Karson are here this time. Hudson musters up a smile and grips Rhondsons hand tightly.

"Thank you, your highness." Hudson says and then looks at Link, who nods at him in assurance.

Link, realizing that there is a chance that there are survivors, hatches a plan. "Granté, I have a favor to ask of you, may I?"

"Sure thing, what's up?" Granté, moving ahead from the crowd, answers.

"There may be some surviving troops, I need you to look for them and then bring them back here."

"No problem. I can handle it."

"Great. Stannis can give you more information as to where he saw them run off to. I'm counting on you." Link says and Granté shakes his hand in compliance. 3 minutes later, Samus arrives in her gunship to pick up the two. Before going, Link asks Greyson and his little brother Pelison if they can do him a favor, handing them some rupees and asking them if he can buy some gold dust from them. They agree and sell it to him, only for Link to then ask them to forge a sword with it and high quality steel, which they also agree to (stressing that this will take time). Samus, overhearing this, asks them to wait a few seconds while she retrieves something from her ship. She comes back with a box of steel called Chozodium, a rare (silvery) metal from planet Zebes that is incredibly strong after being refined, which she offers as the "steel" for the sword. Greyson and Pelison decide to get to work on it right away and the two leave them to their work. Zelda asks what that was about and Samus tells her that it was just a friendly chat while patting her head, to which Zelda straightens out her messed up hair afterwards before following them back to the ship. Granté bids his parents farewell and they wish him luck on his task (Jerrin had given him a bag of supplies and Robbie gave him an ancient short sword to complement his eightfold sword, as well as integrating ancient armor components to his Shiekah attire) as he boards the ship with the others. The townspeople say their goodbyes as the ship takes off before beginning their task of constructing the carriage. At the edge of town, Stannis looks on and silently hopes they can succeed where he and the soldiers failed. The ship flies over Shadow Pass (small wooded area to the northwest of Tarrey Town) and drop Granté off there, Stannis having told them that would be the best place to check since the soldiers ran in that direction.

Granté jumps down from the bottom hatch and grabs a tree branch before somersaulting down. "Good luck you guys!" Granté waves goodbye as the ship flies away towards Eldin.

* * *

 **Eldin, outside the entrance of the south mine**

A small group of about 7 Gorons, lead from behind by Bludo (an elderly Goron with an eyepatch over his right eye, a long white beard with four knots that connect to his bushy white eyebrows, a shackle on his left wrist and hunched over), boss of the Gorons and Yunobo (a Goron youth with a small patch of hair on his head, shackles on his elbows and wrists, a cloth around his neck held by a padlock styled pendent with the Goron symbol and a belt with pouches around his waist), Bludo's assistant and Daruk's grandson.

"We need to leave our brother's someplace safe and then go back for the others." Bludo says to Yunobo, who is holding a drillshaft and has another one on his back to not burden his boss.

"I know. But where can they stay? There's no place we can leave them without getting spotted." Yunobo answers. "Besides, I think it would be better if I went in your stead, you're not really in the best shape, boss."

"Crag stone! I'm not staying in some hole while the rest of our brothers are slaves to that shiny intruder and the Yiga!" Bludo yells out. "Just because you're the champion's grandkid doesn't mean you can do things on your own. Got it?"

"But boss, I'm afraid that if you go, then you'll-" Before Yunobo can finish his sentence, they're interrupted by an elite pirate dropping behind them and roaring. "Rager!" The other Gorons look back and begin to panic as Yunobo grabs a nearby boulder and chucks it at the pirates head, disorienting it and giving him and a Goron enough time to grab Bludo and run down the path. Moments later, the pirate recomposes itself and begins its pursuit…"

 _ **To be continued**_

* * *

 **Author's note: That's not good. So, it's time to head to Eldin and purify Vah Rudania before things get really messed up. Also, to anyone wondering why I picked those unique names for the lieutenant and commander; no real reason (btw, anyone else excited for Game of Thrones season 8 like me?). :P Anyway, I found out that apart from giving the main characters the most importance, it should also be directed at secondary characters because it helps to expand the story and remind you that there are other people with problems of their own, a consequence of the antagonist's actions. Stay tuned for the next one. :)**


	13. Chapter 13 Outpost

**Chapter 13: Outpost**

 _"The people when rightly and fully trusted will return the trust."_ _-Abraham Lincoln_

 **Back in Tarrey Town, the townspeople have begun dismantling parts of the houses that haven't been completely burned in the attack to fashion the wood into a large carriage. Bolson, relieved that the cranes they brought for Hudson had survived the attack, uses them to haul the salvaged guardians from the woods (Hudson, Karson and Greyson push them to a raft and Kapson pulls it towards the town, where Fyson connects the hook onto the guardian where it is then pulled up, rinse and repeat). Robbie and Jerrin take apart the guardians and incorporate them to the carriage. Stannis, meanwhile, stands guard at the towns entrance to make sure they don't get any more intruders. On another side of town, Pelison is overseeing the smelting of the Chozodium while making the mold for the handle for it (Link had left a very particular design).**

"How's it going, little brother?" Greyson walks up to the forge and addresses Pelison.

"Hi big brother. It's taking a while to melt the metal, so I'm making the handle to kill time." Pelison answers, not moving from his spot. "Anyway, how are things with the carriage?"

"It's going. Robbie gave me a break until we need to bring more guardians, so I came here to check on things" Greyson walks up to check on the hearth, adding some heat with the funnel. "Hmm. Give it about two more hours then we can add the gold dust. Got it?"

"Got it, brother!" Pelison agrees while giving a thumbs up, having finished part of the handles mold (a triforce sigil).

* * *

 **Further inside Shadow Pass, Granté continues his search for the surviving soldiers, having picked up the trail but also avoiding monster camps, lengthening his search even more than needed.**

"Hmm, so they did come through here." Granté says to himself, kneeling to check on some old tracks left by the soldiers. "But, which way did they go?" He sees several tracks going in different directions, unsure of which path to take. Hearing rustling sounds from the bushes, Granté readies his eightfold sword and prepares for any eventuality. To his surprise, an exhausted soldier wearing a cloak lumbers out.

"Hey, what's wrong?" Granté addresses the soldier and walks up to him.

"You...You're one of the Sheikah, right?" The soldier, breathlessly, says. "I'm Strand of the Akkala guard. It's good to see someone other than another monster."

"What happened to you?"

"I was separated from my platoon when we escaped the citadel. They shouted to me which way they were going and I've been trying to get to them ever since."

"Well, I'm looking for the others too. There's a safe place for you and the other soldiers, can you take me to them?"

"Of course, I'll lead you." Strand affirms and Granté offers him a shoulder to ease his exhaustion as they move deeper into the forest.

* * *

 **Inside a skull rock by Mendigo Pool (lava, no less), Yunobo and Bludo have holed themselves up after distracting the elite pirate from the other Gorons who ran downhill. The elite pirate begins slamming its fists on the skull rock (its entrances previously covered by rocks).**

"So, we can just hide here until the others get far enough away?" Yunobo says amidst the shaking.

"That, or until it gets bored and just goes after them." Bludo states. "We've got to think of something quick."

The elite pirate backs up and fires its turret, causing the two to lose their footing and having a small boulder dislodges itself and lands on Bludo.

"Argh, my back!" Bludo falls to his knees and tries to calm the pain.

"Hang on, you're gonna be fine, boss!" Yunobo says while trying to help Bludo.

"I can handle it; I'm not your grandpa!" Bludo shouts in disapproval as he get back on his feet, all while straightening himself out. "Alright kiddo, you and I are the only thing standing between that ugly bastard and five of our brothers. So we can hide here or we can take these drillshafts and make him REALLY angry." Yunobo thinks about their situation and decides that they can't just sit and do nothing, so he pushes out the rocks from one of the rocks "eyes" and they both stare at the now observing elite pirate.

"How's your back, boss?"

"Aw, just give me the drillshaft!" Bludo holds the drillshaft and throws it at the elite pirates left shoulder, piercing its hide and angering it.

"Boss, I think he's mad!" Yunobo activates Daruk's Protection and stands in front of Bludo to shield him.

"Alright, come on then, you overgrown lizard!" Bludo shouts, holding the remaining drillshaft as the pirate rips out the other from its shoulder and tosses it aside. It extends its bayonets and prepares to slash at them and just then, a green light shines behind it. Yunobo and Bludo are confused by the lights sudden appearance and the alerted elite pirate stops its attack to inspect it; it sees Samus's gunship hovering just behind (the source of the light being the green windshield). From the bottom hatch, Link drops down and glares at the elite pirate, who in turn roars at him. Link activates his helmet (instead of a hood like shape, it now resembles a blackish grey Spartan hoplite helmet, sans the crest and closed at the mouth), draws his sword and shield and lets the pirate make the first move. The pirate runs at him and Link charges his sword with electricity (giving the blade a yellowish glow with currents moving up and down it). After dodging the pirate's swipe, Link slashes upward, electrocuting it and damaging the pirates chest before upper cutting it with his shield and making it reel back.

"Hahah, go Link!" Yunobo excitedly shouts.

"Come on Champion, give him what for!" Bludo shouts in praise.

The pirate recovers and aims its turret at Link, firing several shots which he effortlessly avoids and parries the last shot at the pirates head. Angered, the elite pirate charges at Link once again, this time grabbing him and then tossing Link at the mountain wall and disorienting him. The pirate menacingly walks towards Link before roaring (as if beckoning) at him as Link gets back up and they both charge at each other. Link, having grabbed the discarded drillshaft, plunges it into the pirates chest, jumps off and snaps his fingers, casting the full force of Urbosa's Fury on the drillshaft (like a lightning rod), shorting out its turret and destroying the pirates organic armor and exposing its blue, veiny flesh and causing it to fall to its knees. Link lands in front of it and powers his sword with fire and slashes downward, only to be blocked by phazon growths that had quickly formed over its exposed flesh. The pirate gets up and then punches him away, having used the burst of phazon corruption to recover damage, then runs one of its bayonets at Link. He holds the sword sideways with both hands (on opposite ends), charges the AKEB, then has the added pressure from the bayonet set off the kinetic energy, sending both of them in the opposite directions. Link swiftly grabs his bow and shoots 3 phazon arrows at the pirate, overloading the growths and bursting the ones on its chest. Using the new boosters on his back, Link jumps up at a 45° angle and slashes down on the stunned elite pirate (sword aflame), severing the top left half of its torso. The pirate falls to the ground and Link walks off to the others, but Yunobo shouts to warn him of the still alive pirate rushing towards him from behind, only for Link to shoot another phazon arrow at its head (without looking, only turning slightly), bursting it and then having its lifeless body fall into the lava. Yunobo and Bludo applaud Link from atop the ship (Samus had previously picked them up) before they disembark, along with Samus and Zelda.

"Link! Aren't you a sight for sore eyes!" Yunobo walks up and greets Link.

"It got hairy there for a sec, thank Din you got here." Bludo comments, patting Link on the back (much to his discomfort).

"We heard about the trouble on the mountain. So, we came to help out." Link states while retracting his helmet.

"Who's 'we'?" Bludo asks, causing Link to gesture at Zelda and Samus. Only until they're in view does Yunobo become surprised at Zelda.

"Wow! What's the princess doing all the way out here?"

"She couldn't sit by and do nothing. So, she's here to add to the effort. Trust me; she's got this." Link says with some confidence at the end of his sentence. As he finishes, Zelda walks up to Yunobo.

"You must be Yunobo. Link has told me much about you." Zelda kindly says, earning a "really?" from Yunobo. "Yes. It was your help that allowed him to appease Vah Rudania and free Daruk's spirit from Ganon's malice. I offer you my thanks."

"Aw, it was nothing your highness." Yunobo says while rubbing the back of his head. "He needed my help and the boss couldn't with his bad back (Bludo gives a "bah!" at that remark).

"I couldn't have made it without your help, you know that." Link smiles and pats Yunobos back, earning a smile from him.

"Hold all the mushy stuff; we need to see if our brothers made it to the cave." Bludo abruptly cuts in. "If you don't mind, your highness. I'm worried about them."

"Yes, you're right. We should confirm their safety first."

"Alright, you two lead the way. Oh Zelda, make sure you finish that elixir for the full 24 hours." Link comments, pointing to the bottle with a grey liquid.

"Do I really have to?" Zelda says with a look of disgust.

"Yes. With it, you'll be able to withstand the heat. Go on now." Link answers with a bit of authority. Zelda pouts before opening up the bottle and, after counting to 3, chugs the whole elixir down. Close by, Samus extends a stake like device from her cannon and drives it into the pirates severed arm (Virginia stating that they need a blood, tissue and bone sample for analysis), afterwards she tells Link and Zelda to take whatever they might need from the ship as they won't be returning for a while, before grabbing the severed limb and tossing it into the lava. Link complies and enters the ship, coming back with some provisions and a large, flat weapon. Samus then has the ship fly up and land on a rocky ledge, taking on the same color and texture of said ledge.

"Alright, no one will be able to see it now." Samus comments to herself as the two Gorons stare in awe over what the ship just performed. Regardless, the two Gorons lead the way to their hiding place and Samus asks Zelda why she looks like she's going to be sick, to which she simply gives her the empty bottle and tries to catch up with the others, exclaiming about the bad taste in her mouth. Samus follows suit, confused.

* * *

 **Back in the cave housing the monsters, Silas returns to inspect them.**

"Well, has there been any change?" Silas asks.

"Yes master, just as the texts indicated, they have changed." The guard answers before leading Silas to the dungeon. Upon opening the door, the monsters had in fact been altered by the malice; they were now silver variants.

"Very good. Now, are the harnesses ready?"

"We've gotten several prepared." The guard holds up a metallic harness with prongs jutting out of them. "If what our informant says is true, they can become stronger still if the silver monsters are struck by lightning."

"Hmm, have a handful of monsters harnessed and then sent to Thundra Plateau. Afterwards, our master is to be notified."

"Master Silas!" Another footsoldier hurriedly runs to Silas before kneeling down. "I have urgent news from Akkala!"

"Speak quickly." Silas orders.

"Master Ghor was defeated in battle and the orange ship was seen flying towards Eldin!"

Silas grits his teeth in frustration after coming to the realization. "They've found out about the crystals and that witch is still alive…"

"Perhaps we should change our plans, master?"

"No, nothing is going to change." Silas angrily answers. "You are to take the monsters to Thundra Plateau. I will not tolerate any more setbacks, is that understood?"

The Yiga present acknowledge him and prepare to harness the monsters while Silas runs off to Eldin to find the trio.

* * *

 **Granté and Strand make their way to Skull Lake in the northwestern parts of Akkala.**

Is this where you said they were?" Granté asks, looking around the lakeshore.

"Yes. This is the place they told me that they'd hide at." Strand answers and, as if to confirm it, several soldiers pop out disguised with bushes and dirt and have bows armed on the two, demanding that they disarm themselves.

"Hold it! I'm with one of your guys, Strand!" Granté shouts and after a few minutes of apprehension, they lower their bows.

"Sorry about that. We couldn't take any chances." One of the soldiers speaks up. "It's good to see someone other than those freaks."

"Well, I can assure you, Link sent me to find you." Granté says, causing the soldiers to be surprised at the revelation that Link is here. "It's good that I ran into Strand, thanks for telling him where you were. Otherwise I'd be going in circles."

"What?" The soldier asks in disbelief. "Lieutenant Stannis told us, Strand included, to run towards Skull Lake. Strand said he'd lead the Yiga away and that was the last we saw of him. How did you get away from them?"

"What are you talking about?" Granté asks in confusion. Strand smiles maliciously, removes his cloak (revealing five bloody holes on his armor), removes Granté's eightfold sword and holds him from behind while holding the sword to his throat.

"Hands down." Strand orders Granté, not wanting him to grab the ancient short sword on his back and he complies. He then looks at the other soldiers (who have set their bows on him), his eyes turning from brown to blue. "Not one shot, or I'll kill him."

"You're one of them?!" Granté exclaims in surprise and anger.

"For a Sheikah, you're not too bright. Now, I order you all to lower your weapons and prepare to be judged by the Yiga. Or have this man's death on your conscience."

"Forget about me! Shoot him!"

Strand moves the sword closer to keep Granté quiet and begins going on a tirade about how it's futile to fight against the phazon and that all should allow themselves to be corrupted. During this, Granté signals the soldier closest to them by tapping his right palm with his left index finger. The lead soldier acknowledges this and during Strand's rant, he shoots him in the hand, causing him to shout in pain and drop the sword. Granté grabs the sword, kicks Strand to the ground and runs it through his heart. Strand's face goes from anger to regret as his eyes turn back to their original color before exhaling his last breath. The soldiers lower their heads in remorse. After regaining his composure and shutting Strand's eyes, Granté tells the surviving soldiers of Stannis and Mormont being at Tarrey Town and that's where they should go. With two soldiers carrying Strand's body, Granté and the others make the long walk back to Tarrey Town.

* * *

 **Gorko Tunnel**

"You guys cut through the cliffs just to get to this tunnel?" Link asks, concerned over the fact that they had to make the mostly hazardous trek to Gorko Tunnel.

"Of course, brother!" Gonguron, a Goron refugee with a yellow construction hat and blue loincloth, speaks up. "We can use it to hide more of our brothers when we get them here."

"Plus, there's plenty of food here for all of us." Bladon, a Goron with a light red loincloth and knot top, as well as Gonguron's brother, cuts in. "You haven't lived until you've tried one of my roasts! Hahah!"

Link remembered that the last time he came here; he had to bring a rock sirloin so that Bladon could prepare it for his brother so he could reveal an ancient shrine hidden here. If Gonguron's boost of energy afterwards was any indication, the refugees would be all kinds of elated to have "prime rock" in their bellies.

"I guess you're right. As long as you all can find a hiding spot without going hungry is worth the risk." Link comments with a smile.

"You've got a point too, this place is very roomy and- ahh! Ahh!" Samus exclaims after removing her helmet and hastily putting it back on after being singed by the extreme heat. "What is that?! The air is boiling!"

"Hahah! You didn't take any elixirs like the princess?" Bludo jokingly laughs. "How did you manage without being toasted like a steak?"

Samus realizes that her environmental hazard warning didn't go off because she is already wearing her varia suit (extreme heat and cold resistance). Then she looks to Zelda, who is completely unbothered by the heat. "How are you not burning?"

"Remember that bottle I handed you?" Zelda asks, to which Samus nods. "It had a fireproof elixir. Paya tweaked the formula a bit so that they could last a full 24 hours instead of 10 to 14 minutes. They were in the basket she gave us, remember?"

"Ah, that's right. Could I try one?"

"Go ahead, fair bit of warning; it tastes like moblin sweat." Zelda hands her a bottle from the provisions Link brought, grimacing from remembering how she downed the other bottle. Samus removes her helmet, cringing slightly from the heat again, and takes a sip from the bottle. To her surprise, she can't feel the heat anymore and continues drinking the blackish-grey liquid.

"You know, it's not bad." Samus comments, much to Zelda's shock.

* * *

 **Later after sunset, the team explained what is happening and the Gorons explain that after the barrier went up, the Yiga and a slew of monsters came by and started attacking their city and snatching up people. It was only until afterwards that the "Ragers" started appearing. Yunobo says that while he was underground, he saw about five Yiga surrounding a pod and, while making hand gestures, formed a Rager inside the pod after they put in this "weird bottle of gunk" in it. Samus concludes that the Yiga can use the pods, known as genesis chambers, to cultivate the "ragers" or rather Elite Pirates, by means of their magic, phazon and whatever is inside those bottles. They also explain that the barrier, for them at least, came from divine beast Vah Rudania and that it was surrounded by ragers when they last ran away. The team plan to make their way to the mountain summit and cleanse Vah Rudania, but due to the nightfall they decide to hold off until the morning for better visual.**

"Well, it's not much, but you three can make yourself at home for now." Bludo says while sitting down and heaving a big sigh. "I'm just gonna wait until chow is ready."

"Link, since we're going to spend the night here, do you mind if I take the slate and check on the people in Tarrey Town? With the shrine here, I can teleport back without having to run into trouble."

"Hmm, fine." Link hands her the slate, but quickly takes it back. "But, come RIGHT BACK after you've finished. No sightseeing, no checking on peculiar things and no wandering. Understood?"

"Yes, mother." Zelda sarcastically remarks at Links commands. Link hands her the slate and she tells the others that she'll be back in a moment.

"I already set the travel medallion to the center of town; you need to only press the icon and you'll be there in no time." Link says while indicating the area on the map. Zelda nods and presses the icon, dispersing into millions of particles that fly up and through the roof.

"Where do you guys get those wonderful toys?" Samus muses aloud, having deactivated her suit due to the elixirs protection, and sitting on a rock.

"Alright brothers!...and sister. The roasts are ready, come and get it!" Bladon proudly shouts, causing Yunobo, Gonguron and the other three refugees to rush over and feast. Link decides to wait for Zelda to return, in hopes that she'll bring some food from town. Samus, however, decides to indulge on the roasts, little does she know…

"Alright, I haven't had sirloin in years." Samus says while rubbing her hands in anticipation. "Let me at the- huh?" Samus stops abruptly at seeing that the sirloins are actually _rocks in the shape of meat with a bone through it._

"Mm, help yourself!" Gonguron hands her a roast while munching on his own.

"You know, I'm trying to watch my figure. I'll wait for Zelda to bring something with less….gravel." Samus quickly refuses the rock roast.

"Aw, you don't know what you're missing!" Gonguron continues eating with his brothers and having a good time. Samus walks back to join Link, who is trying to contain his laughter.

"Shut up…"

They both notice Yunobo walking up to Bludo, bringing him a rock roast. "Here you go, boss."

"Hahah, thanks kiddo." Bludo warmly receives Yunobo's offering. "You're always worrying about me, aren't you?"

"Aw, it's nothing boss. You looked out for me since I was little, it's the least I can do."

"Your gramps would be thrilled to see us now; we were sworn brothers after all." Bludo says before taking a bite from the roast. "Has it really been 100 years?"

'Yeah, doesn't look it, huh boss?"

"Hmm." Bludo lowers the roast and has a sad expression. "I miss him, you know? He always had my back when we were young, we promised to look out for each other. But, the Calamity came and….I couldn't hold up my end."

"Boss." Yunobo places his hand on Bludo's shoulder. "I'm sure he would've wanted you to be safe, along with all of us. Besides, I'm here now."

Bludo looks at Yunobo and smiles. "Yeah, thank Din for that." Bludo then goes back to eating his roast. Link and Samus overhear the conversation and can't help but smile. Link then turns to the weapon covered by a cloth that he brought in and decides that it's time.

* * *

 **Zelda arrives at Tarrey Town, feeling queasy from the sensation of being split into millions of pieces and then put back together. Before she can do anything, a resident runs into her in fear.**

"Wait! What's going on?"

"Princess? There's a group of bokoblins on the bridge!" The resident points to the bridge, with a group of four corrupted bokoblins surrounding a soldier. Upon further inspection, it's revealed to be commander Mormont.

"Come on, you beasts! I'll send you all back to hell!" Commander Mormont swings his royal claymore at one of the bokoblins, knocking it off the bridge and the other three swarm him. Shouting in frustration, he buckles under the pressure until an arrow hits one of the bokoblins on the head. Seizing the opportunity, commander Mormont slashes a third bokoblin in half and the other is impaled through the chest. With the monsters dead, he falls to his knees and is approached by Zelda, who had shot the arrow earlier.

"Commander Mormont, do you have some sort of death wish?"

"You don't understand your highness!" Commander Mormont shouts in frustration. "We're the ones who are supposed to protect the citizens, not be protected by them." The other residents look at him with remorse over his declaration. "We are here to serve the people and we do nothing. _I_ do nothing; and my men pay the price. They were wiped out by these monsters; I can't stop just because I'm wounded! Someone has to pay for this!" Seeing that his wounds are getting more severe, Zelda offers him a shoulder and helps him back to town and into the inn where he can rest.

"I understand your suffering, Commander. But, this won't do you any good if you die in vain. Please, just rest and recover, these people need you." Zelda grabs his hand and tries to get through to him, only for Mormont to look away. Stannis comes in and helps him onto the bed, where Kapson can tend to his wounds. Afterwards, Stannis and Zelda walk out to talk and hear Mormont's last agonized words before he falls asleep.

"I couldn't save...my men…"

Outside and in the center of town, Stannis tells Zelda that the carriage is almost complete and that Fyson went to the South Akkala Stable to bring some horses to pull it, Granté had found the remaining soldiers (making emphasis on what happened to Strand) and that Greyson wants to speak with her afterwards.

"Why didn't the other soldiers offer assistance?" Zelda asks.

"Commander Mormont told us to stay in the town in case the monsters got through. He even went so far as to threaten us with prison time for insubordination if we joined in the fight." Stannis looks back at the inn where Mormont is recuperating at before turning back to face Zelda. "I guess he's tired of all the loss and he'd rather risk his own life instead of ours."

Zelda looks back to the inn as well, saddened by the burden that Mormont placed on his own shoulders. She then has Stannis promise to make sure that he doesn't do something like this again, this time it's _her_ orders. Stannis agrees and confirms in a way that sends a chill down her spine: "Of course, _Queen's orders."_ Zelda stays prone for 5 seconds then hastily walks away, leaving Stannis confused. Zelda walks over to Robbie and Jerrin who tell her that the carriage is nearly complete (being 4 carriages of wood, reinforced with guardian parts for extra protection), the fact that they had been working together round the clock saved a lot of time. Hearing this gave Zelda some peace of mind and took it off off...other things. Finally, Greyson arrives to speak with Zelda.

"Princess! Good timing, we just finished it not too long ago." Greyson says while handing her an object covered in a worn out cloth. "Sorry, we didn't have better wrappings, but the contents are great."

"We both made it, but I made the sheath!" Pelison says, excited to hear what Zelda has to say about it.

"What is this?" Zelda asks in confusion, unwrapping it and then becoming shocked by what it is; a rapier with a silvery grey handle, the cross guard taking the form of a gold, circular design with the triforce symbol in the center, a whitish pink wing design on the side and the blade concealed by a blue sheath. She pulls it out to see the blade silvery steel with golden diamonds running down it).

"Not bad, right? Link had us make it for you and that steel is some seriously strong stuff."

"Where did the tall lady get it from? I want to know!" Pelison chimes in, leaving Zelda with a few questions; Link had the sword made for her? Samus made sure that was forged with steel not native to Hyrule?

"I...I will ask her for you. Thank you for your work." Zelda smiles after strapping the rapier to her waist. "Now, I really must be going, we must prepare to venture to Vah Rudania." Zelda waves goodbye to everyone and uses the slate to return to Gorko Tunnel. Before this, she looks out past the barrier to see a Lynel pacing back and forth. Could this be the same one from Lanayru? She remembers that after the metroids were destroyed, it ran off. Shaking the thought from her mind, she teleports back.

* * *

"Link, are you sure you should be giving this to me?" Yunobo asks after Link returned the large weapon he had; a large, flat blade that spreads out at the top with intricate markings along with the Goron symbol, a brown metallic edge at the top, a brown guard that resembles half of a gear, a long blue handle and a pommel that also resembles a half gear. This is the Boulder Breaker, Daruk's personal weapon.

"Of course, it was your grandfathers after all. Besides, you'd make better use of it." Link says.

"What do you mean?"

Link sits down on a stone and leans on his arm. "Well, Bludo told me that it was you who started that escape attempt from the mines; you even punched an elite pirate in the face, according to Bladon. Am I wrong?"

"In the face? I definitely would've wanted to see that." Samus comments with a smile.

Yunobo, flustered by the pair's comments, scratches the back of his head and chuckles. He passes it off as just luck. Link, however, thought otherwise; He knew what he had to do, so Yunobo stood up and opposed the invaders, exactly what Daruk would've done. Link once again passes Boulder Breaker to Yunobo, who only looks at it. "You're a hero, Yunobo. Your grandfather would be very proud of you, like I am."

Yunobo stares at it for a few seconds, then finally takes his grandfather's weapon, rests it on his right shoulder and gives a big ear to ear grin. The moment is slightly hampered by Bludo's loud snoring, causing Link and Yunobo to laugh quietly.

From the shrine, Zelda materializes (again feeling nauseous from the travel) and quietly walks past the sleeping Gorons. Upon reaching Link, Yunobo and Samus (asleep), she sits down next to her knight and places her sword on her lap.

"Everyone is fine, aside from a few bokoblins. Nothing that the soldiers couldn't handle." Zelda recounts her experience, omitting commander Mormont's lone defense. "Now, I think we should talk about this."

Link looks at her new sword and smiles. "They did a great job, gold dust and that "Chozodium" made a fine looking blade. I should thank Samus for it later."

"Why though? Instead of a regular sword we could get anywhere, why make one instead?"

Link sheaths the sword and explains to Zelda about the small chat he had with Samus after they brought her back to the ship to heal her from the zeta metroids attack; Link won't always be around to protect her, so he should instead prepare her for any eventuality. The idea for the sword was actually on his mind for several weeks prior, only now did he decide to follow through. Zelda thanks him for the sword, but puts special emphasis on not being separated from him regardless. Immediately afterwards, she leans her head on his right shoulder, asking him if he promises to not leave her behind, on the battlefield or otherwise. Link, although surprised by her action, answers her directly. "I promise."

Yunobo, having witnessed this, smiles at the two before bidding them good night as he lies down next to Bludo to sleep. Link answers him then says the same to Zelda, only to see that she's already fast asleep (still leaning on him). He looks around to see everyone else sleeping (the refugees sleeping close to each other near the shrine, Samus leaning against the wall) and decides to do the same. Though, on thought goes through his mind beforehand; "wait, she didn't bring any food?"

* * *

"Are you sure about this?" Samus asks Virginia, having woken up first.

"Yes, the pirates from Hyrule field, Akkala citadel and last night have the exact same genetic code." Virginia answers Samus's inquiry, confirming that all the elite pirates faced thus far have identical DNA, leaving only one logical conclusion; they're clones. The question now is where the Yiga got the DNA from? Although, through deduction, it shouldn't be that hard to conclude. Minutes later, everyone else wakes up and the group plans their next course of action; head through the mines and free any enslaved Gorons, all while making their way to Death Mountain summit where Vah Rudania is stationed. Armed and ready, the three bid their friends goodbye and begin their trek to the southern mines. As they continue, Yunobo stops them to join the quest, having been given Bludo's blessing to go. Link pats his shoulder and welcomes him to the party. From the tunnel, Bludo looks on and prays that Daruk protects them, especially Yunobo.

"Take care of your grandkid, brother."

* * *

"I see them." Link announces, having made it to the cliffs overlooking the southern mines, referring to the Gorons in chains and mining the black phazon crystals.

"It's awful, they don't look healthy." Zelda comments, taking note of their sickly appearances.

"They hardly fed us. Double shifts with little rest too." Yunobo adds, a little frustration present in his voice. "Not anymore."

"Hang on, I'm picking up something." Samus zooms in to the entrance, switching visors to detect anything odd (Thermal visor: overloaded by the heat. Dark visor: no dark creatures detected. Echo visor: only sounds from pickaxes and walking elite pirates detected. X-Ray visor: several chameleon like creatures near the entrance and walls). "There! I see several creatures camouflaged on the walls; I think you call them lizalfos."

"What? Yunobo, how did you get past those?" Link asks.

"We didn't; they weren't here before." Yunobo retorts, surprised by the heightened security.

"Get down!" Zelda rushes everyone to duck behind some rocks, having heard noises around them. The origin of the noise is revealed; a corrupted guardian stalker, scanning the area with its rotating head before walking off. From above, corrupted guardian skywatchers patrolling the perimeter. With the coast clear, the group breaks cover.

"Ok, those _definitely_ weren't here before."

"Why? Why is there so much in the way?" Zelda asks in frustration.

Link contemplates the situation before coming to a conclusion; they know they're coming. Not wanting a repeat with Vah Ruta, the Yiga decided not to take any chances and pulled out all the stops.

"This is going to be tougher than I thought…"

 _ **To be continued**_

* * *

 **Authors note: Now things get interesting. A few things about this chapter, I wanted to showcase how Link has gotten better in fighting the newer enemies and that he can utilize the Champion's abilities in a much more practical way, Zelda got a new sword forged with steel not from this world (yes, I made up the name Chozodium, it just rolls of the tongue, hahah) and modelled after the gleaming rapier from Hyrule Warriors to show that Link has more trust in her to protect herself, the connection that Yunobo and Bludo have aside from boss and apprentice and commander Mormont's regret for what happened at the citadel. Now, what comes next is how to get to Vah Rudania. See you soon. :)**


	14. Chapter 14 Infiltration

**Chapter 14: Infiltration**

"A secret's worth depends on the people from whom it must be kept." -Carlos Ruiz Zafon

 **The group had managed to reach the southern mines, only to be once again impeded by high security in the area, no doubt the Yiga having been notified of their approach. Regardless, the group had come up with a possible answer to their problem.**

"We really don't have much of a choice, do we?" Link halfheartedly asks.

"Not if you want zero casualties to the Gorons. Our only choice is to walk among them." Samus answers, concluding that they must disguise themselves.

"That's very dangerous. Unless we have their clothes, at least, we won't be getting close." Zelda comments, looking over the sentries posted at the entrance.

"I thought about that. Yunobo, you were there with the others, did you manage to see what was inside their store rooms?"

"Hmm, the one near the left of the entrance had the pickaxes to mine the crystals. Next to that is the forge to make them into weapons and I never saw what was in the rest." Yunobo answers.

"There has to be more uniforms in one of those store rooms. We'll never know until we check."

"Hold on, what exactly are you implying?" Link asks, before realizing Samus's intentions. "You seriously want to go down there alone?!"

"Not entirely. You three will be my eyes while I sneak into one of those store rooms." Samus says before she deactivates her suit. "Can you do that?"

Reluctantly, the others agree and Samus descends the cliffs, keeping away from the skywatchers spotlights. Thankfully, the blue glow from the barrier partially hides her zero suit, giving her a bit more cover. Timing the skywatcher patrol, she sneaks by the lights and reaches the back of the store rooms (around the perimeter of the mines).

"Alright, show me the good stuff." Samus says to herself as she scans the rooms for uniforms (hiding every so often the skywatchers fly overhead). On the fifth room, she sees several boxes with garments and Yiga masks (Samus: Ah, there you are!) and, after hiding one more time, materializes her arm cannon and activates the blow torch like apparatus (from the plasma beam) and makes a square hole in the back of the room, big enough for her to fit through. Quickly, she jumps through, just barely missing the skywatcher. Once inside, Samus places a box in front of the hole to not raise suspicion, and she searches the other boxes for uniforms that'll fit her and the others. After finding two for Link and Zelda (she had their measurements jotted down), she just needed to find one for herself. Her search is interrupted by sounds from outside, causing her to lean her head against the door.

"So, all this just for three idiots?" A Yiga footsoldier asks.

"It's not just three _idiots,_ you fool." A Yiga archer, adjusting a duplex bow on his shoulder, retorts. "The champion, princess and outsider; they're the ones who ruined our outpost and Metroid breeding ground in Lanayru. Remember?"

"Oh, right. But, this seems like a bit much, don't you think?"

"We can't take any more chances; the mining operation is going as planned and the source is protected inside of Vah Rudania."

"Source? You mean what we use to make the elite pirates?"

"Yes."

"How did the supreme master get it?"

"Well, from what I hear…" Samus, clearly interested in how the elite pirates are created, decides to listen in. Unfortunately she doesn't notice the mask sliding from her arm, which falls to the ground, making noise. "What was that?"

"It came from that room."

The one of the guards enters the store room with a blue phazite sickle ready, but doesn't find anyone. Nevertheless, he checks the inside a bit and finds the mask on the ground, concluding that it fell off one of the racks. Seeing the box was moved, he creeps up and slashes behind it, finding nothing again. From above, Samus lodged herself on the roof (feet on one wall, hands on a rafter across), having used the box as a stepping stone, making it look as if someone went through it.

"Did you find anything?"

"Hmm, no. I think a mask just fell off." The guard answers, putting the box back in its place before walking out and closing the door. "Anyway, what were you saying?

"Oh, that. You know what; it's in the files in the watchtower on the left of the entrance. Check for yourself when you get the chance; its better explained there."

Samus quietly gets back on the floor, recovers a new mask and checks the boxes one more time. Finding a Yiga Blademaster uniform (known for being taller than others), she takes it and runs back through the hole she made. While welding the piece back, a skywatcher closes in on her, making her worry. Before its spotlight reaches her, the skywatcher becomes alerted to a rock thrown at it and shines the light at the direction it came from. After a few seconds, it continues its route and Samus makes it back to the others.

"Good arm."

"It was nothing." Yunobo answers with a big smile.

"So, how'd it go?" Link asks.

"I got the uniforms, it looks like we can wear them over our clothes; meaning we can discard them on the way." Link and Zelda nod in acknowledgement. "Also, they seem to have some files that I need to have a look at; they're getting the materials for the elite pirates from somewhere specific."

"How will we find those files?" Zelda asks, clearly intrigued by the idea of learning new information.

"It's in the left watchtower at the entrance. One of us needs to get up there without raising suspicion, the only question is; how?"

"We'll figure it out once we see the inside of the mining station, for now, we should get going." Link says while, having deactivated his suit, puts on the Yiga garb over his champions tunic. Samus and Zelda follow him as well by putting on their own garbs. Link and Zelda decide to leave behind their weapons with Yunobo, who will stay behind until they give the signal. A few minutes later of traversing the cliffs, to appear that they came from the regular path, the three reach the entrance to the mining station, where they are stopped by the sentries.

"Hold!" A Yiga footsoldier stationed at the entrance stops the trio. "What are you doing here?"

Link, not wanting either of the girls to say anything to put them on the spot (Zelda in particular because of her accent), speaks up. "My name is Ravio, Master Silas sent us from the Lanayru outpost to offer security services." Link answers in a gruff voice.

"Lanayru? I thought that outpost was destroyed."

"It was, that is why he sent us."

"Hmm." The footsoldier stares at the other two and addresses them. "Where are your weapons?"

"Uh, those were left behind, for maintenance." Link hastily answers.

"I didn't ask you, young man." The footsoldier sternly says, before turning his attention back to the others. Link begins tensing up because the Yiga is looking directly at Zelda. "Well? What's the story?"

"The exact same one he just told you." Zelda replies, hiding her accent in a more smooth, but reproachful voice. "We left them behind to be repaired and Master Silas told us to pick up the new weaponry as replacements. In case you're wondering, yes; we mean the phazite weapons made from the crystals you've been mining." Link is visibly impressed at Zelda's act, so he steps back to let her continue. "Now, do you have any more questions or are you done wasting our time?"

"Take it easy, I just needed to ask. Your arrival just confused me."

"Hey, I understand. It's just that Master Silas is in a very bad mood and it wouldn't be best to upset him anymore than he already is. Wouldn't you agree?"

"Point taken. Alright, let me assign you three to your tasks; Ravio, you are to patrol the mining operation and report any suspicious activity.

"Understood." Link answers.

"You are to stand guard on the watchtower left of the entrance. Stop anyone trying to get in without authorization. Also, what was your name?"

"Understood sir and my name is Hilda." Zelda answers, hiding her contentment of being assigned to the tower with the files.

"And you...what's your name?"

"Malkovich, sir." Samus answers with a distinct Irish accent.

"Malkovich? What kind of name is that?" The Yiga asks in a fairly derisive tone.

"It's a traditional name; only the strongest fighter in our house has the honor of carrying the name." Samus then moves in close so that her mask and the guards mask are a few inches apart. "And I won't tolerate you deriding it."

"No need to get testy." The guard holds up his hands to diffuse the tension. "Very well, Malkovich; your assignment is to guard the watchtower at the exit to the mines, report any suspicious activity to your superiors at once."

The three have been given their orders and are now able to enter the southern mines. Upon entering, they look on in shock over the unfavorable conditions that the gorons are working in (blisters on their hands and feet, whip marks on their bodies which are most likely phazon burns, the young ones harnessed and forced to drag the carts with pickaxes or harvested crystals and several others being whipped for lagging behind. Steeling themselves, they continue to the shack where the phazite weapons are being held and take what they need (Link: vicious sickle. Zelda: demon carver and duplex bow. Samus: windcleaver). After taking the weapons, Samus hands the others a pair of communicators to keep in touch (on their ears and hidden by their masks) and they separate to their designated areas ( **A/N:** the three events happen at the same time.)

* * *

 **Link**

While patrolling the mine and looking out for any possible weaknesses in the area, Link muses to himself over the irony of wearing Yiga attire. His musings are immediately interrupted by the sounds of guards shouting to a goron miner for dropping a cart of crystals. Before they can whip the terrified goron, Link steps in to "do the deed".

"I'll handle it; you go about your business." The other Yiga laugh as Link strong-arms the goron away. After those same Yiga walk away, Link (behind some rocks) takes his mask off so that the goron can realize that it's him. The goron quickly tells him that there's no real escape due to sentries at several points, the skywatchers patrol the perimeter round the clock and the fire breath lizalfos blend into the walls, so they're hard to spot. Link assures him that they're here to help and will find a way to get them all out. For now, he just needs the gorons to hold out for as much as they can, to which he nods. Keeping up the charade, he escorts the goron back and orders him to pick up the pace while yelling at other onlookers (What are you looking at? Get back to work!). The other Yiga laugh at his act while Link internally apologizes for his harshness, promising to get everyone out of here, somehow. For now, Link continues his "patrol'.

* * *

 **Zelda**

Upon reaching the watchtower, Zelda relieves the other guard to take his place. After he leaves, she takes the opportunity to look over the files there.

"Hmm, patrol routes...checkpoints...weapon shipments...project helix! Alright, let's have a look."

 _ **With the information given to us by Master Ridley, we have been able to successfully create "elite pirates" to add to our forces. Two months ago, a creature called a space pirate by our God came to our world. When she was regaining consciousness after Calamity Ganon's defeat, our God captured it after it decided to wander the caves and kept the space pirate in seclusion in hopes that it would yield information on our world for her, but saw other possibilities when she regenerated Master Ridley.**_

 _ **Combat notes: The elite pirates possess tremendous strength and agility. They follow orders to the letter and carry out any mission with great efficiency. A new feature, according to Master Ridley, is the application of a red phazon core, allowing the elite pirate to mutate into a stronger form should it take excessive damage; with strengthened phazon armor and increased ferocity.**_

"I should make notes of this; captured space pirate, Ridley regenerated (Samus may want to know about this), red phazon. Now, let's put all of you away. Hmm?" As Zelda puts the files back into their respective places, one file in particular catches her attention; titled "The Giant".

 _ **Considered the pinnacle of project helix, this particular elite pirate is in a league all its own. Possessing double the strength of your basic elite pirate, The Giant can also use phazon to regenerate damaged tissue and organs (so long as there is some of the organ left) as well as increases in durability, muscle mass, stamina and intelligence among other things.**_

 _ **Combat notes: Apart from physical strength and firepower, The Giant is also equipped with a red phazon core, allowing it to mutate if it is grievously injured. This is the point where all praise for it becomes fear; upon mutating, its strength multiplies even further, but its intelligence dwindles to that of a rampaging monster. In this state, it attacks both friend and foe alike. We have lost many of our personnel and monster forces to the first one in its berserker state, only after our God destroyed it did the rampage end. These creatures are to be only used as the last resort; anyone who has seen the rampaging Giant never lives to tell about it.**_

"First one? Then, there's another of these 'Giants'?"

Zelda jots all the important points down and puts the files away to not raise suspicion. Just as she puts the last one away, a guard walks in to ask if there have been any oddities yet. After answering that there haven't been any, the guard leaves to let her continue.

"Alright, we've got the information we need." Zelda walks up to the window and looks out into the station. "Now, how do we get the gorons out?" As she wonders this, she is suddenly brought out of her thoughts by the sound of large wings flapping through the sky. She looks up and a cold chill runs down her spine.

* * *

 **Samus**

"Alright, so Goron city isn't that far from here, but there's a large metal wall blocking the way." Samus says, looking at a map of Eldin. "Also, how many hostiles are there?"

There are 17 Yiga, 8 elite pirates, 5 guardian stalkers, 7 pairs of fire breath lizalfos and 6 guardian skywatchers." Virginia gives her report.

"Hmm, the gunship could maneuver around the skywatchers, but the stalkers would all aim at the same time. But, the real problem is how to get the prisoners out of here?"

Before she can ponder any further, a large flapping sound catches her attention, followed by a loud roar. Looking up, she sees Ridley flying overhead, still disbelieving his appearance in this land.

"I do believe that _he_ is an even bigger problem, Samus." Virginia says, causing Samus to huff in frustration. "I haven't figured out how to deal with the hostiles yet, but I may have an idea for an escape route."

"Really? And what is that?"

"That metal gate will take a while to cut through with the blowtorch, but if we use _that,_ then we could destroy it and any hostile in front of it.

Samus listens to Virginia's suggestion, taking into account that using _that_ would take 5 minutes to charge AND that she needs to have her suit fully activated as well, blowing her cover. Sighing, Samus contacts Link and says that she needs a distraction. Unfortunately, before anymore can be said, a large three fingered hand plummets down from the roof, grabs Samus and pulls her out.

"Did you really think that I wouldn't find you skulking around here?" Ridley says in amusement before ripping off Samus's mask and hood.

"How did you know?" Samus demands, the frustration present in her voice.

"I'd never forget your scent, even among all of this mountain's embers; I'll always be able to single you out." After answering, Ridley roars to bring the other Yiga to attention. After bringing her down, three footsoldiers tie her to a post (one of them being Link to assure her that she's got him for back-up). Afterwards, the soldiers (after moving the gorons to a corner) move aside and Silas walks over to Samus.

"Ms. Aran, it's funny how we keep running into each other like this."

"Let me off of this thing and I'll show you how funny it can get." Samus says, seething in anger.

"Oh, I wager you could show me. But, I have other matters to attend to. Now, the princess and her knight; where are they?" Silas demands, only to be met with silence. "Surely you don't expect me to believe that you split up to hide your tracks? I'm well aware that you three move collectively, so (Silas pulls out his red phazite windcleaver and points it at Samus's neck) where are they?"

Samus looks to the side and answers. "I wouldn't know."

Frustrated, Silas sheathes his sword, harshly grabs Samus by the face and turns her head to look at him. "You know, you've been pushing me to the boiling point recently. You made me look like a fool to our master! You three stopped our attack on Kakariko village, destroyed the metroid breeding ground, had the audacity to defy us in Zora's Domain and now you're here to stop the mining of these crystals, aren't you?!"

"Don't get so angry, you'll age quicker." Samus mockingly says while smirking.

"Why, you insolent little-" Silas extends his right arms claws and prepares to impale her before being stopped by Ridley.

"Silas. Haven't you figured it out yet? She's clearly staling our time, there's no need to interrogate her for their whereabouts; they're among us, aren't they?"

Ridley's affirmation makes Samus's eyes light up in alarm and she discreetly looks at Link. Seeing this, Link slowly backs away without calling attention to himself.

"I see. Well then, let us in on the charade; which ones are they?" Silas calmly asks, to which Samus stays quiet. "No? Very well then; I'll just assume that this was a joint effort with the gorons. Pirates, guardians! Take aim!" Silas commands and they all aim at the terrified gorons. Samus and Link begin panic, Zelda looks from the watchtower in horror without any idea as to what to do and Yunobo only watches helplessly from the cliffs. "Fire-"

"No, wait! Wait!" Link steps forward, takes off his mask and throws to the ground before pulling off his hood. "I'm here."

Silas holds up his fist, signaling them to stop. He then walks over to Link, disarming him and staring intently. "Unwilling to make sacrifices, aren't you? Had you stayed down, you might have been able to get away."

"Only you would hide behind innocents, they're not going to pay for our actions." Link says in quiet anger, causing Silas to smile.

"Heheheh, spare me your indignation. Now, where is the princess?"

"I sent her away, she's long gone by now." Link says to the unamused Silas, having told Zelda to run off and regroup with Yunobo (slaying a couple of lizalfos in her way with arrows).

"Well, she couldn't have gotten far, we'll get her later. But first, there's the matter of what to do with you-" Before Silas could finish his sentence, a large boulder falls down near them, followed by another one. Looking to the east, they see Yunobo chucking them to draw their attention and before they can react, fireballs pelt the guardian stalkers, disrupting their sensors. Ridley looks to the west and sees Zelda (unmasked) as the cause of the fireballs and flies off towards her. Making use of the commotion, Link beats two of the guards with his fists, grabs a sickle and cuts Samus's ropes, allowing her to roundhouse kicks Silas onto a cart of crystals. Avoiding guardian and elite pirate fire, Link and Samus duck behind some boulders and the latter activates her suit, calling her ship to offer cover fire. As this happens, the lizalfos shoot fireballs at the pair and the guardians lay a barrage of shots, followed by the elite pirates. Using Daruk's Protection, Link shields himself and Samus from the attacks, not knowing what else they can do with their quickly diminishing shield. Just then, Yunobo jumps down and collides his own protection with Link's, causing a shockwave that knocks back all of the attackers. After both dispel their barriers, Yunobo hands Link his weapons and, as the Yiga recompose themselves, he reactivates his suit (flaking off the disguise in the process) and prepares for battle.

* * *

On the western side of the mines, Zelda shoots at Ridley with phazon arrows, slightly damaging his armorskin.

"Raah… Let me show you real fire!" Ridley inhales deeply before firing a stream of superheated energy from his mouth. In response, Zelda uses her barrier to block and redirect the stream onto Ridley's chest. "How are you doing that?! You have no shield generator!"

"It's a power given to the royal family by the gods, this one in particular is called Nayru's Love; I'll throw back anything you throw at me." Zelda answers in a defiant tone.

Before Ridley can retort, Samus's gunship (remote control) flies overhead and fires at the hostiles, destroying several guardian stalkers and breaking away the cell doors that had the prisoners contained. Deciding that the primary threats are in the mines, Ridley abandons the fight, with a swing of his tail at Zelda (knocking her against the quarry wall), and flies up to attack the ship. After getting back to her feet, Zelda shakily pulls out the duplex bow and aims a phazite arrow at Ridley. Exhaling, she lets loose the arrow, breaking off a joint on his left wing before he can strike the ship. Screeching in pain, Ridley hovers down before he crashes and he directs an elite pirate to go after Zelda. Seeing this, Yunobo swings the boulder breaker at the lizalfos in the way and calls out to Zelda, throwing a drillshaft into the wall a few inches away from her. Reaching it, she sees her rapier and lynel bow tied to it and frees them from the shaft before looking at Yunobo, who nods at her before returning to battle. After strapping it back to her waist, the elite pirate catches up and growls menacingly at her, who unsheathes her rapier and demon carver in response.

* * *

Link and Samus, back to back, fight off the footsoldiers and lizalfos while the ship offers suppressing fire on the larger monsters (including Ridley). Some of the gorons have decided to aid in the fight, led by Yunobo, and use their tools as weapons. A Yiga tries to blindside Yunobo, but another goron swings his pickaxe horizontally and the footsoldier ducks down. Swinging vertically, the footsoldier slashes horizontally, disintegrating the pickaxe with the phazite blade and leaving the goron open to a deep slash across his chest and he falls to the ground, lifeless. No time to mourn, Yunobo punches the footsoldier into the rocks nearby and prepares for an incoming guardian stalker and lizalfos.

"3 minutes and 15 seconds remain, Samus." Virginia gives the report on _that_ being charged.

"Copied." Samus answers before returning fire to the elite pirates. Link charges his AKEB and slams it into a boulder, sending it flying towards one of the elite pirates, sending it careening towards a watchtower and collapsing it on some lizalfos. Frustrated, Ridley sends out a loud roar, making a cliff wall collapse. The rockslide is revealed to be a corrupted Igneo Talus Titan (double the size of an average one, a vaguely humanoid appearance and the stone parts connected by thick, phazon ligaments).

"Oh damn…" Link and Samus collectively say as they witness the monster.

* * *

Zelda struggles with the elite pirate, losing the duplex bow in the lava below. The pirate shoots at her, missing by inches as she ducks behind some rocks. Arming a phazite arrow, she quickly moves out of cover and shoots at the pirate's shoulder cannon, destroying it. Roaring, the pirate charges at her with its bayonets ready and Zelda puts up her barrier and the pirate swings at it. Nayru's Love protects her, but its incomplete formation knocks the both of them in opposite directions, with the added consequence of Zelda dropping her rapier. The elite pirate recovers first and walks towards her, but Zelda shoots another phazite arrow at its face, stunning it and giving her time to run at her rapier. Getting the arrow out, the elite pirate extends its right bayonet and charges at Zelda again, who reaches her rapier, charges it with Din's Fire, turns around and sends a fiery slash at the pirates neck, decapitating it mere inches away from her. The bayonet drives into the wall to the left of Zelda before deactivating and the elite pirates body falls down next to her, much to her relief. Seeing the Igneo Talus Titan, she pulls of her tattered Yiga disguise (her regular attire underneath) and runs off to face it with the others.

* * *

With its new ligaments, the Talus swings its "arms" as if they were flails, catching several lizalfos and guardian in its wake (due to its mindless instinct still present) and the two do their best to dodge the swing.

"Link, exactly how do we destroy this thing?" Samus asks, the exhaustion present in her voice.

"There should be an ore deposit on its body. But, this one doesn't seem to have any." Link answers while tossing remote bombs at the Talus' head. In response, Samus scans the beast and finds a large ore deposit within its torso (or rather central stone). At the same time, Virginia informs her that "that" has finished charging and Samus immediately decides to us it to bust through the Talus' fiery stone hide.

"Link, distract it for 20 seconds, I have a plan. When I say move, get clear of the Talus."

"I'm on it." Using Revali's Gale, Link launches himself upward and tosses a remote bomb at its "head", provoking it into swinging at him and, at that moment, Zelda uses her power to restrain it. 20 seconds later, Samus shout at them to get away. Aiming at the Talus, her cannon muzzle opens up into a group of concentric rings.

"Zero laser; ready to fire." Virginia confirms as a large stream of bluish white energy releases from Samus's cannon. Yunobo and the others stare in awe as the laser digs into the Talus' torso. After 7 seconds, the laser dissipates and Samus's cannon reverts to its regular state and the Talus drops to its knees, exposing a large ore deposit.

"Impressive." Zelda comments after dispelling her barrier covering Link and herself.

"Maybe next time you should start with that one." Link jokingly adds.

"Yeah, I can only use it once every three days. It takes a strain on the suit." Samus says while checking her suits diagnostics.

"Samus, look out!" Yunobo shouts as Silas barely misses slashing Samus from behind with his windcleaver. Link shouts that he and Zelda will handle the Talus, Yunobo and the surviving Gorons fend off the Yiga and elite pirates and the ship employs hit and run tactics on the remaining guardians and the still grounded Ridley.

"Link, I have an idea; shoot a phazite arrow at the left shoulder when I say. Got it?"

"Got it." Link uses ice arrows to cool down the monsters fiery surface and, with the added thermal shock, bombards its ore deposit with arrows. In response, the Talus prepares to swing its arm once again; prompting Zelda to shout "now!" and Link shoots a phazite arrow at the extended phazon ligament on its shoulder, severing the arm. Zelda, taking the sheikah slate off of Links belt, uses the stasis rune to freeze it in place and quickly instructs Link to send her up in the air with Revali's Gale and she rapidly shoots arrows at a specific point to add as much kinetic energy as possible before falling down onto Links arms. The stasis cancels out and the arm slams into the gate blocking the exit like a rocket, destroying it.

"Hurry, get to the exit!" Zelda shouts as she gets back on her feet. Yunobo offers backup as the more injured gorons hobble to the exit. Link has Zelda lead them away as he helps Yunobo fend off the attackers. Meanwhile, Samus continues her rematch with Silas.

"This is the last time you make a fool out of me!" Silas angrily shouts as he alternates between his windcleaver and bladearm. Samus, no longer blinded by frustration like last time, effortlessly evades all attacks.

"You let yourself be swayed by a promise of power; you were always a fool." Samus disappointedly retorts, causing Silas to angrily shoot a phazon blast from his arm. Samus answers his attack with the wavebuster, allowing the surges to travel through Silas blast, electrocuting him. While he's stunned, Samus uses her boost ball to ricochet off of him several times before ending in a screw attack across his chest. Just before landing, Ridley intercepts and swipes at her against the wall.

"Silas had his chance, it's my turn now!" Ridley, with his damaged but regenerating wing, flies up and drags Samus against the rocky surface, disrupting her suits stability. The Talus comes to and takes a swing at her with its remaining arm, hitting Ridley as well. The two fall to the ground, Samus trying to stabilize her suit and Silas approaches her with his sword aimed at her heart.

"Be a good girl and stay dead this time." Silas spitefully says before being hit by an arrow through his right leg. As he screams from the pain, Samus takes the opportunity to fan kick him against a crystal deposit, stabbing him several times. Samus grabs his sword and javelin throws it at his abdomen, making him cough up blood and lose consciousness. Leaving her suit deactivated, she runs off to rejoin Zelda (the one who shot the arrow) and they help the gorons get away. Elsewhere, Link and Yunobo hold off the Yiga and elite pirates with both showing signs of fatigue. The Talus makes one final attempt to crush everybody there, but Yunobo has Link charge his AKEB and strike Yunobo with his barrier up into the Talus chest, who strikes the ore deposit and grabs on, punching what remains of it. With a mighty swing of the boulder breaker, the ore deposit shatters, ending the Talus' life. As it falls on the cliffside, it releases extreme heat which makes the stones forming the wall unstable as it disintegrates. Upon landing, Link and Yunobo fist bump in glee. Looking to the exit, they see the others beckoning them to escape. As they run, Yunobo is hit with a stray guardian shot, propelling him to the wall. Link calls out to him before running to offer assistance. The Lizalfos gang up on him, but he slashes at each one that tries to slow him down. Feeling overwhelmed, he conjures Urbosa's Fury, raining down lightning on all of the attackers and allowing him to reach Yunobo.

"Can you walk?"

"Yeah. That was a cheap shot though." Yunobo retorts, causing Link to laugh a little. Helping him up, they see the remaining forces glare at them as they're boxed in. Thinking through their ideas, the enemies close in on the pair. Samus tries to get her ship to fire, but it was forced to land due to overheating. Looking behind him, Yunobo orders Link to jump on his back as he curls up, not explaining what he intends to do. Summoning Daruk's Protection, he propels Link upward as the monsters rush them and, moving quickly, Yunobo uses all his might and slams his fists onto the unstable wall, causing a tremendous rock slide.

"Yunobo! No!" Link shouts as he gets clear of the falling rocks that engulf the monsters, including Ridley (who was unable to get away). Silas regains consciousness as he shouts in alarm before being crushed by the rocks. The dust settles and Link floats down with his paraglider to witness the entire mine destroyed. Panicking, he tries to move away the rocks to try and find Yunobo, before realizing that there are ones that are too heavy for him to lift. Falling to his knees, he hangs his head in shame over failing to protect his friends' grandson. Zelda walks up to him and comforts Link.

"Link, you did all you could. If it wasn't for him, his people couldn't have escaped from their torment. Please, let us continue to Vah Rudania for his sake." Zelda sadly but resolutely says.

Link looks her in the eye before speaking. "I understand. Let's finish this for him. I won't fail you, brother." Link gets to his feet and walks back to the escapees with Zelda. Lagging behind, Samus hears the rumbling of stones as Ridley erupts from the other side of the rocks. Samus spitefully promises that they'll have their rematch before leaving with the others as Ridley stumbles out before turning his head in their direction and roars in anger.

* * *

 **Thundra Plateau**

The Yiga, having brought several silver monsters with metallic harnesses, capture a golden lynel which was turned into this from a lightning strike. After binding it, the footsoldiers move away for Dark Samus to approach. Dark Samus digs her index finger into its forehead, corrupting it and increasing its overall strength even further, much to her sadistic delight.

 _ **To be continued**_

* * *

 **Author's note: ok, I'll be honest; I didn't like writing this chapter that much. It blocked my ideas SO MUCH that it took me this long to write it. Anyway, sorry for the delay guys, I know there are plenty of followers who were waiting anxiously for this story to be updated. I hope to get the next one out sooner than this one. On a side note, I know that BotW 2 is on the way, but this will be its own story because there is next to nothing for me to incorporate from it (a teaser trailer really isn't enough to go on, heheh). If they show some other things in the coming months, then I MIGHT consider it.**

 **Now, to the reviewer under the name Tanner, will I incorporate the resurrection of Ganondorf in this story? My answer is: I dunno, wait and see. :P**

 **See you soon, guys. :)**


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